Upgrade notifications for issue searching and dupe handling

when there is a parse error

docs/advanced/configuration.md

@@ -11,32 +11,34 @@ value of a namespaced config key with `atom.config.get`:
 @showInvisibles() if atom.config.get "editor.showInvisibles"
 ```
 
-Or you can use the `::subscribe` with `atom.config.observe` to track changes
-from any view object.
+Or you can subscribe via `atom.config.observe` to track changes from any view
+object.
 
 ```coffeescript
+{View} = require 'space-pen'
+
 class MyView extends View
-  initialize: ->
-    @subscribe atom.config.observe 'editor.fontSize', (newValue, {previous}) =>
-      @adjustFontSize()
+  attached: ->
+    @fontSizeObserveSubscription =
+      atom.config.observe 'editor.fontSize', (newValue, {previous}) =>
+        @adjustFontSize()
+
+  detached: ->
+    @fontSizeObserveSubscription.dispose()
 ```
 
 The `atom.config.observe` method will call the given callback immediately with
 the current value for the specified key path, and it will also call it in the
-future whenever the value of that key path changes.
+future whenever the value of that key path changes. If you only want to invoke
+the callback when the next time the value changes, use `atom.config.onDidChange`
+instead.
 
-Subscriptions made with `::subscribe` are automatically canceled when the
-view is removed. You can cancel config subscriptions manually via the
-`off` method on the subscription object that `atom.config.observe` returns.
-
-```coffeescript
-fontSizeSubscription = atom.config.observe 'editor.fontSize', (newValue, {previous}) =>
-  @adjustFontSize()
-
-# ... later on
-
-fontSizeSubscription.off() # Stop observing
-```
+Subscription methods return *disposable* subscription objects. Note in the
+example above how we save the subscription to the `@fontSizeObserveSubscription`
+instance variable and dispose of it when the view is detached. To group multiple
+subscriptions together, you can add them all to a
+[`CompositeDisposable`][composite-disposable] that you dispose when the view is
+detached.
 
 ### Writing Config Settings
 
@@ -48,10 +50,9 @@ but you can programmatically write to it with `atom.config.set`:
 atom.config.set("core.showInvisibles", true)
 ```
 
-You can also use `setDefaults`, which will assign default values for keys that
-are always overridden by values assigned with `set`. Defaults are not written
-out to the the `config.json` file to prevent it from becoming cluttered.
+If you're exposing package configuration via specific key paths, you'll want to
+associate them with a schema in your package's main module. Read more about
+schemas in the [config API docs][config-api].
 
-```coffeescript
-atom.config.setDefaults("editor", fontSize: 18, showInvisibles: true)
-```
+[composite-disposable]: https://atom.io/docs/api/latest/CompositeDisposable
+[config-api]: https://atom.io/docs/api/latest/Config

docs/advanced/globals.md

@@ -1,34 +0,0 @@
-# Globals
-
-Atom exposes several services through singleton objects accessible via the
-`atom` global:
-
-* atom
-  * workspace:
-      Manipulate and query the state of the user interface for the current
-      window. Open editors, manipulate panes.
-  * workspaceView:
-      Similar to workspace, but provides access to the root of all views in the
-      current window.
-  * project:
-      Access the directory associated with the current window. Load editors,
-      perform project-wide searches, register custom openers for special file
-      types.
-  * config:
-      Read, write, and observe user configuration settings.
-  * keymap:
-      Add and query the currently active keybindings.
-  * deserializers:
-      Deserialize instances from their state objects and register deserializers.
-  * packages:
-      Activate, deactivate, and query user packages.
-  * themes:
-      Activate, deactivate, and query user themes.
-  * contextMenu:
-      Register context menus.
-  * menu:
-      Register application menus.
-  * pasteboard:
-      Read from and write to the system pasteboard.
-  * syntax:
-      Assign and query syntactically-scoped properties.

docs/advanced/view-system.md

@@ -1,58 +0,0 @@
-## Atom's View System
-
-### SpacePen Basics
-
-Atom's view system is built around the [SpacePen] view framework. SpacePen
-view objects inherit from the jQuery prototype, and wrap DOM nodes
-
-View objects are actually jQuery wrappers around DOM fragments, supporting all
-the typical jQuery traversal and manipulation methods. In addition, view objects
-have methods that are view-specific. For example, you could call both general
-and view-specific on the global `atom.workspaceView` instance:
-
-```coffeescript
-atom.workspaceView.find('atom-text-editor.active') # standard jQuery method
-atom.workspaceView.getActiveEditor()      # view-specific method
-```
-
-If you retrieve a jQuery wrapper for an element associated with a view, use the
-`.view()` method to retrieve the element's view object:
-
-```coffeescript
-# this is a plain jQuery object; you can't call view-specific methods
-editorElement = atom.workspaceView.find('atom-text-editor.active')
-
-# get the view object by calling `.view()` to call view-specific methods
-editorView = editorElement.view()
-editorView.setCursorBufferPosition([1, 2])
-```
-
-Refer to the [SpacePen] documentation for more details.
-
-### WorkspaceView
-
-The root of Atom's view hierarchy is a global called `atom.workspaceView`, which is a
-singleton instance of the `WorkspaceView` view class. The root view fills the entire
-window, and contains every other view. If you open Atom's inspector with
-`alt-cmd-i`, you can see the internal structure of `WorkspaceView`:
-
-![WorkspaceView in the inspector][workspaceview-inspector]
-
-#### Panes
-
-The `WorkspaceView` contains `prependToBottom/Top/Left/Right` and
-`appendToBottom/Top/Left/Right` methods, which are used to add Tool Panels. Tool
-panels are elements that take up screen real estate not devoted to text editing.
-In the example above, the `TreeView` is appended to the left, and the
-`CommandPanel` is appended to the top.
-
-```coffeescript
-# place a view to the left of the panes
-atom.workspaceView.appendToLeft(new MyView)
-
-# place a view below the panes
-atom.workspaceView.appendToBottom(new MyOtherView)
-```
-
-[spacepen]: http://github.com/nathansobo/space-pen
-[workspaceView-inspector]: https://f.cloud.github.com/assets/1424/1091631/1932c2d6-166b-11e3-8adf-9690fe82d3b8.png

docs/apm-rest-api.md

@@ -30,6 +30,8 @@ All requests that take parameters require `application/json`.
 Parameters:
 
 - **page** (optional)
+- **sort** (optional, values: `created_at`, `updated_at`, `downloads`)
+- **direction** (optional, values: `asc`, `desc`)
 
 Returns a list of all packages in the following format:
 ```json
@@ -57,6 +59,20 @@ Link: <https://www.atom.io/api/packages?page=1>; rel="self",
       <https://www.atom.io/api/packages?page=2>; rel="next"
 ```
 
+By default, results are sorted by download count, descending.
+
+#### GET /api/packages/search
+
+Parameters:
+
+- **q** String query to search
+- **sort** (optional, values: `created_at`, `updated_at`, `downloads`)
+- **direction** (optional, values: `asc`, `desc`)
+
+Returns a list of all packages in the same format as `/api/packages`.
+
+By default, results sorted by relevance to search query.
+
 ### Showing package details
 
 #### GET /api/packages/:package_name

docs/creating-a-package.md

@@ -40,7 +40,7 @@ package.json files have their own additions.
 - `main` (**Required**): the path to the CoffeeScript file that's the entry point
 to your package
 - `stylesheets` (**Optional**): an Array of Strings identifying the order of the
-stylesheets your package needs to load. If not specified, stylesheets in the
+style sheets your package needs to load. If not specified, style sheets in the
 _stylesheets_ directory are added alphabetically.
 - `keymaps`(**Optional**): an Array of Strings identifying the order of the
 key mappings your package needs to load. If not specified, mappings in the
@@ -119,27 +119,27 @@ Also, please collaborate with us if you need an API that doesn't exist. Our goal
 is to build out Atom's API organically based on the needs of package authors
 like you.
 
-## Stylesheets
+## Style Sheets
 
-Stylesheets for your package should be placed in the _stylesheets_ directory.
-Any stylesheets in this directory will be loaded and attached to the DOM when
-your package is activated. Stylesheets can be written as CSS or [LESS] (but LESS
-is recommended).
+Style sheets for your package should be placed in the _stylesheets_ directory.
+Any style sheets in this directory will be loaded and attached to the DOM when
+your package is activated. Style sheets can be written as CSS or [LESS] (but
+LESS is recommended).
 
 Ideally, you won't need much in the way of styling. We've provided a standard
 set of components which define both the colors and UI elements for any package
-that fits into Atom seamlessly. You can view all of Atom's UI components by opening
-the styleguide: open the command palette (`cmd-shift-P`) and search for _styleguide_,
-or just type `cmd-ctrl-shift-G`.
+that fits into Atom seamlessly. You can view all of Atom's UI components by
+opening the styleguide: open the command palette (`cmd-shift-P`) and search for
+_styleguide_, or just type `cmd-ctrl-shift-G`.
 
-If you _do_ need special styling, try to keep only structural styles in the package
-stylesheets. If you _must_ specify colors and sizing, these should be taken from
-the active theme's [ui-variables.less][ui-variables]. For more information, see the
-[theme variables docs][theme-variables]. If you follow this guideline, your package
-will look good out of the box with any theme!
+If you _do_ need special styling, try to keep only structural styles in the
+package style sheets. If you _must_ specify colors and sizing, these should be
+taken from the active theme's [ui-variables.less][ui-variables]. For more
+information, see the [theme variables docs][theme-variables]. If you follow this
+guideline, your package will look good out of the box with any theme!
 
-An optional `stylesheets` array in your _package.json_ can list the stylesheets
-by name to specify a loading order; otherwise, stylesheets are loaded
+An optional `stylesheets` array in your _package.json_ can list the style sheets
+by name to specify a loading order; otherwise, style sheets are loaded
 alphabetically.
 
 ## Keymaps
@@ -157,9 +157,9 @@ loaded in alphabetical order. An optional `keymaps` array in your _package.json_
 can specify which keymaps to load and in what order.
 
 
-Keybindings are executed by determining which element the keypress occurred on. In
-the example above, `changer:magic` command is executed when pressing `ctrl-V` on
-the `.tree-view-scroller` element.
+Keybindings are executed by determining which element the keypress occurred on.
+In the example above, `changer:magic` command is executed when pressing `ctrl-V`
+on the `.tree-view-scroller` element.
 
 See the [main keymaps documentation][keymaps] for more detailed information on
 how keymaps work.
@@ -195,7 +195,8 @@ with your package that aren't tied to a specific element:
 ```
 
 To add your own item to the application menu, simply create a top level `menu`
-key in any menu configuration file in _menus_. This can be a JSON or [CSON] file.
+key in any menu configuration file in _menus_. This can be a JSON or [CSON]
+file.
 
 The menu templates you specify are merged with all other templates provided
 by other packages in the order which they were loaded.

docs/customizing-atom.md

@@ -118,7 +118,6 @@ You can open this file in an editor from the _Atom > Open Your Config_ menu.
       - `cr`: Carriage return (for Microsoft-style line endings)
       - `eol`: `\n` characters
       - `space`: Leading and trailing space characters
-  - `normalizeIndentOnPaste`: Enable/disable conversion of pasted tabs to spaces
   - `preferredLineLength`: Identifies the length of a line (defaults to `80`)
   - `showInvisibles`: Whether to render placeholders for invisible characters (defaults to `false`)
   - `showIndentGuide`: Show/hide indent indicators within the editor

docs/index.md

@@ -18,7 +18,6 @@
 * [Developing Node Modules](advanced/node-modules.md)
 * [Keymaps](advanced/keymaps.md)
 * [Serialization](advanced/serialization.md)
-* [View System](advanced/view-system.md)
 * [Scopes and Scope Descriptors](advanced/scopes-and-scope-descriptors.md)
 
 ### Upgrading to 1.0 APIs

docs/your-first-package.md

@@ -49,7 +49,7 @@ Register the command in _lib/ascii-art.coffee_:
 ```coffeescript
 module.exports =
   activate: ->
-    atom.workspaceView.command "ascii-art:convert", => @convert()
+    atom.commands.add 'atom-workspace', "ascii-art:convert", => @convert()
 
   convert: ->
     # This assumes the active pane item is an editor
@@ -57,10 +57,10 @@ module.exports =
     editor.insertText('Hello, World!')
 ```
 
-The `atom.workspaceView.command` method takes a command name and a callback. The
-callback executes when the command is triggered. In this case, when the command
-is triggered the callback will call the `convert` method and insert 'Hello,
-World!'.
+The `atom.commands.add` method takes a selector, command name, and a callback.
+The callback executes when the command is triggered on an element matching the
+selector. In this case, when the command is triggered the callback will call the
+`convert` method and insert 'Hello, World!'.
 
 ## Reload the Package
 
@@ -95,13 +95,13 @@ you don't need it anymore. When finished, the file will look like this:
   'cmd-alt-a': 'ascii-art:convert'
 ```
 
-Notice `atom-text-editor` on the first line. Just like CSS, keymap selectors *scope* key
-bindings so they only apply to specific elements. In this case, our binding is
-only active for elements matching the `atom-text-editor` selector. If the Tree View has
-focus, pressing `cmd-alt-a` won't trigger the `ascii-art:convert` command. But
-if the editor has focus, the `ascii-art:convert` method *will* be triggered.
-More information on key bindings can be found in the
-[keymaps](advanced/keymaps.html) documentation.
+Notice `atom-text-editor` on the first line. Just like CSS, keymap selectors
+*scope* key bindings so they only apply to specific elements. In this case, our
+binding is only active for elements matching the `atom-text-editor` selector. If
+the Tree View has focus, pressing `cmd-alt-a` won't trigger the
+`ascii-art:convert` command. But if the editor has focus, the
+`ascii-art:convert` method *will* be triggered. More information on key bindings
+can be found in the [keymaps](advanced/keymaps.html) documentation.
 
 Now reload the window and verify that the key binding works! You can also verify
 that it **doesn't** work when the Tree View is focused.

exports/atom.coffee

@@ -6,6 +6,7 @@ module.exports =
   BufferedNodeProcess: require '../src/buffered-node-process'
   BufferedProcess: require '../src/buffered-process'
   GitRepository: require '../src/git-repository'
+  Notification: require '../src/notification'
   Point: Point
   Range: Range
   Emitter: Emitter
@@ -32,7 +33,7 @@ unless process.env.ATOM_SHELL_INTERNAL_RUN_AS_NODE
   Object.defineProperty module.exports, 'WorkspaceView', get: ->
     deprecate """
       Requiring `WorkspaceView` from `atom` is no longer supported.
-      Use `atom.view.getView(atom.workspace)` instead.
+      Use `atom.views.getView(atom.workspace)` instead.
     """
     require '../src/workspace-view'
 
@@ -43,7 +44,7 @@ unless process.env.ATOM_SHELL_INTERNAL_RUN_AS_NODE
         `{$} = require 'space-pen'`
         or
         `$ = require 'jquery'`
-      Add `"space-pen": "^3"` to your package dependencies.
+      Add `"space-pen": "^4"` to your package dependencies.
       Or add `"jquery": "^2"` to your package dependencies.
     """
     $
@@ -53,7 +54,7 @@ unless process.env.ATOM_SHELL_INTERNAL_RUN_AS_NODE
       Requiring `$$` from `atom` is no longer supported.
       Please require `space-pen` instead:
         `{$$} = require 'space-pen'`
-      Add `"space-pen": "^3"` to your package dependencies.
+      Add `"space-pen": "^4"` to your package dependencies.
     """
     $$
 
@@ -62,7 +63,7 @@ unless process.env.ATOM_SHELL_INTERNAL_RUN_AS_NODE
       Requiring `$$$` from `atom` is no longer supported.
       Please require `space-pen` instead:
         `{$$$} = require 'space-pen'`
-      Add `"space-pen": "^3"` to your package dependencies.
+      Add `"space-pen": "^4"` to your package dependencies.
     """
     $$$
 
@@ -71,7 +72,7 @@ unless process.env.ATOM_SHELL_INTERNAL_RUN_AS_NODE
       Requiring `View` from `atom` is no longer supported.
       Please require `space-pen` instead:
         `{View} = require 'space-pen'`
-      Add `"space-pen": "^3"` to your package dependencies.
+      Add `"space-pen": "^4"` to your package dependencies.
     """
     View
 
@@ -118,8 +119,8 @@ unless process.env.ATOM_SHELL_INTERNAL_RUN_AS_NODE
     require 'react-atom-fork'
 
   Object.defineProperty module.exports, 'Reactionary', get: ->
-    deprecate "Please require `reactionary` instead: `Reactionary = require 'reactionary'`. Add `\"reactionary\": \"^0.9\"` to your package dependencies."
-    require 'reactionary'
+    deprecate "Please require `reactionary-atom-fork` instead: `Reactionary = require 'reactionary-atom-fork'`. Add `\"reactionary-atom-fork\": \"^0.9\"` to your package dependencies."
+    require 'reactionary-atom-fork'
 
 Object.defineProperty module.exports, 'Git', get: ->
   deprecate "Please require `GitRepository` instead of `Git`: `{GitRepository} = require 'atom'`"

package.json

@@ -1,7 +1,7 @@
 {
   "name": "atom",
   "productName": "Atom",
-  "version": "0.149.0",
+  "version": "0.153.0",
   "description": "A hackable text editor for the 21st Century.",
   "main": "./src/browser/main.js",
   "repository": {
@@ -17,10 +17,10 @@
       "url": "http://github.com/atom/atom/raw/master/LICENSE.md"
     }
   ],
-  "atomShellVersion": "0.19.2",
+  "atomShellVersion": "0.19.4",
   "dependencies": {
     "async": "0.2.6",
-    "atom-keymap": "^2.2.2",
+    "atom-keymap": "^2.3.0",
     "bootstrap": "git+https://github.com/atom/bootstrap.git#6af81906189f1747fd6c93479e3d998ebe041372",
     "clear-cut": "0.4.0",
     "coffee-script": "1.7.0",
@@ -29,7 +29,7 @@
     "emissary": "^1.3.1",
     "event-kit": "0.7.2",
     "first-mate": "^2.2.0",
-    "fs-plus": "^2.3.1",
+    "fs-plus": "^2.3.2",
     "fstream": "0.1.24",
     "fuzzaldrin": "^2.1",
     "git-utils": "^2.1.5",
@@ -39,12 +39,13 @@
     "jasmine-tagged": "^1.1.2",
     "jquery": "^2.1.1",
     "less-cache": "0.19.0",
+    "marked": "^0.3",
     "mixto": "^1",
     "mkdirp": "0.3.5",
     "nslog": "^1.0.1",
     "oniguruma": "^3.0.4",
     "optimist": "0.4.0",
-    "pathwatcher": "^2.3.2",
+    "pathwatcher": "2.3.2",
     "property-accessors": "^1",
     "q": "^1.0.1",
     "random-words": "0.0.1",
@@ -57,57 +58,58 @@
     "season": "^1.0.2",
     "semver": "2.2.1",
     "serializable": "^1",
-    "space-pen": "3.8.1",
+    "space-pen": "3.8.2",
     "temp": "0.7.0",
-    "text-buffer": "^3.6.1",
+    "text-buffer": "^3.7.2",
     "theorist": "^1.0.2",
     "underscore-plus": "^1.6.1",
     "vm-compatibility-layer": "0.1.0"
   },
   "packageDependencies": {
-    "atom-dark-syntax": "0.22.0",
-    "atom-dark-ui": "0.39.0",
+    "atom-dark-syntax": "0.23.0",
+    "atom-dark-ui": "0.42.0",
     "atom-light-syntax": "0.22.0",
-    "atom-light-ui": "0.33.0",
+    "atom-light-ui": "0.36.0",
     "base16-tomorrow-dark-theme": "0.22.0",
     "base16-tomorrow-light-theme": "0.5.0",
     "solarized-dark-syntax": "0.23.0",
     "solarized-light-syntax": "0.13.0",
     "archive-view": "0.37.0",
-    "autocomplete": "0.33.0",
+    "autocomplete": "0.33.1",
     "autoflow": "0.18.0",
     "autosave": "0.18.0",
     "background-tips": "0.17.0",
     "bookmarks": "0.30.0",
     "bracket-matcher": "0.62.0",
     "command-palette": "0.28.0",
-    "deprecation-cop": "0.14.0",
+    "deprecation-cop": "0.18.0",
     "dev-live-reload": "0.35.0",
-    "encoding-selector": "0.7.0",
+    "encoding-selector": "0.8.0",
     "exception-reporting": "0.20.0",
     "find-and-replace": "0.147.0",
     "fuzzy-finder": "0.60.0",
     "git-diff": "0.43.0",
     "go-to-line": "0.26.0",
     "grammar-selector": "0.37.0",
-    "image-view": "0.40.0",
+    "image-view": "0.42.0",
     "incompatible-packages": "0.10.0",
     "keybinding-resolver": "0.20.0",
     "link": "0.26.0",
     "markdown-preview": "0.110.0",
     "metrics": "0.39.0",
+    "notifications": "0.4.0",
     "open-on-github": "0.30.0",
     "package-generator": "0.32.0",
     "release-notes": "0.36.0",
     "settings-view": "0.161.0",
-    "snippets": "0.56.0",
-    "spell-check": "0.43.0",
-    "status-bar": "0.46.0",
+    "snippets": "0.57.0",
+    "spell-check": "0.44.0",
+    "status-bar": "0.48.0",
     "styleguide": "0.30.0",
     "symbols-view": "0.68.0",
     "tabs": "0.56.0",
     "timecop": "0.23.0",
-    "tree-view": "0.132.0",
+    "tree-view": "0.134.0",
     "update-package-dependencies": "0.6.0",
     "welcome": "0.19.0",
     "whitespace": "0.26.0",
@@ -115,13 +117,13 @@
     "language-c": "0.31.0",
     "language-coffee-script": "0.38.0",
     "language-css": "0.23.0",
-    "language-gfm": "0.53.0",
+    "language-gfm": "0.54.0",
     "language-git": "0.9.0",
     "language-go": "0.19.0",
     "language-html": "0.26.0",
     "language-hyperlink": "0.12.0",
     "language-java": "0.11.0",
-    "language-javascript": "0.43.0",
+    "language-javascript": "0.45.0",
     "language-json": "0.8.0",
     "language-less": "0.18.0",
     "language-make": "0.12.0",
@@ -140,7 +142,7 @@
     "language-text": "0.6.0",
     "language-todo": "0.13.0",
     "language-toml": "0.14.0",
-    "language-xml": "0.24.0",
+    "language-xml": "0.25.0",
     "language-yaml": "0.20.0"
   },
   "private": true,

spec/atom-reporter.coffee

@@ -3,6 +3,7 @@ _ = require 'underscore-plus'
 {convertStackTrace} = require 'coffeestack'
 {View, $, $$} = require '../src/space-pen-extensions'
 grim = require 'grim'
+marked = require 'marked'
 
 sourceMaps = {}
 formatStackTrace = (spec, message='', stackTrace) ->
@@ -110,7 +111,8 @@ class AtomReporter extends View
     for deprecation in deprecations
       @deprecationList.append $$ ->
         @div class: 'padded', =>
-          @div class: 'result-message fail deprecation-message', deprecation.message
+          @div class: 'result-message fail deprecation-message', =>
+            @raw marked(deprecation.message)
 
           for stack in deprecation.stacks
             fullStack = stack.map ({functionName, location}) ->

spec/atom-spec.coffee

@@ -5,9 +5,6 @@ Package = require '../src/package'
 ThemeManager = require '../src/theme-manager'
 
 describe "the `atom` global", ->
-  beforeEach ->
-    atom.workspaceView = atom.views.getView(atom.workspace).__spacePenView
-
   describe 'window sizing methods', ->
     describe '::getPosition and ::setPosition', ->
       it 'sets the position of the window, and can retrieve the position just set', ->
@@ -35,6 +32,9 @@ describe "the `atom` global", ->
 
   describe "window:update-available", ->
     it "is triggered when the auto-updater sends the update-downloaded event", ->
+      # FIXME: We need to figure out a way minus workspaceView to handle update-available events.
+      atom.workspaceView = atom.views.getView(atom.workspace).__spacePenView
+
       updateAvailableHandler = jasmine.createSpy("update-available-handler")
       atom.workspaceView.on 'window:update-available', updateAvailableHandler
       autoUpdater = require('remote').require('auto-updater')

spec/config-spec.coffee

@@ -554,11 +554,13 @@ describe "Config", ->
     describe "when the config file contains invalid cson", ->
       beforeEach ->
         spyOn(console, 'error')
+        spyOn(atom.notifications, 'addError')
         fs.writeFileSync(atom.config.configFilePath, "{{{{{")
 
       it "logs an error to the console and does not overwrite the config file on a subsequent save", ->
         atom.config.loadUserConfig()
         expect(console.error).toHaveBeenCalled()
+        expect(atom.notifications.addError.callCount).toBe 1
         atom.config.set("hair", "blonde") # trigger a save
         expect(atom.config.save).not.toHaveBeenCalled()
 
@@ -692,7 +694,6 @@ describe "Config", ->
             expect(atom.config.get(['.source.ruby'], 'foo.bar')).toBe 'baz'
             expect(atom.config.get(['.source.ruby'], 'foo.scoped')).toBe true
 
-
     describe "when the config file changes to omit a setting with a default", ->
       it "resets the setting back to the default", ->
         fs.writeFileSync(atom.config.configFilePath, "foo: { baz: 'new'}")

spec/fixtures/packages/package-with-activation-commands/index.coffee

@@ -9,5 +9,6 @@ module.exports =
     atom.commands.add 'atom-workspace', 'activation-command', =>
       @activationCommandCallCount++
 
-    atom.workspaceView.getActiveView()?.command 'activation-command', =>
+    editorView = atom.views.getView(atom.workspace.getActiveEditor())?.__spacePenView
+    editorView?.command 'activation-command', =>
       @legacyActivationCommandCallCount++

spec/notification-manager-spec.coffee

@@ -0,0 +1,57 @@
+NotificationManager = require '../src/notification-manager'
+
+describe "NotificationManager", ->
+  [manager] = []
+
+  beforeEach ->
+    manager = new NotificationManager
+
+  describe "the atom global", ->
+    it "has a notifications instance", ->
+      expect(atom.notifications instanceof NotificationManager).toBe true
+
+  describe "adding events", ->
+    addSpy = null
+
+    beforeEach ->
+      addSpy = jasmine.createSpy()
+      manager.onDidAddNotification(addSpy)
+
+    it "emits an event when a notification has been added", ->
+      manager.add('error', 'Some error!', icon: 'someIcon')
+      expect(addSpy).toHaveBeenCalled()
+
+      notification = addSpy.mostRecentCall.args[0]
+      expect(notification.getType()).toBe 'error'
+      expect(notification.getMessage()).toBe 'Some error!'
+      expect(notification.getIcon()).toBe 'someIcon'
+
+    it "emits a fatal error ::addFatalError has been called", ->
+      manager.addFatalError('Some error!', icon: 'someIcon')
+      expect(addSpy).toHaveBeenCalled()
+      notification = addSpy.mostRecentCall.args[0]
+      expect(notification.getType()).toBe 'fatal'
+
+    it "emits an error ::addError has been called", ->
+      manager.addError('Some error!', icon: 'someIcon')
+      expect(addSpy).toHaveBeenCalled()
+      notification = addSpy.mostRecentCall.args[0]
+      expect(notification.getType()).toBe 'error'
+
+    it "emits a warning notification ::addWarning has been called", ->
+      manager.addWarning('Something!', icon: 'someIcon')
+      expect(addSpy).toHaveBeenCalled()
+      notification = addSpy.mostRecentCall.args[0]
+      expect(notification.getType()).toBe 'warning'
+
+    it "emits an info notification ::addInfo has been called", ->
+      manager.addInfo('Something!', icon: 'someIcon')
+      expect(addSpy).toHaveBeenCalled()
+      notification = addSpy.mostRecentCall.args[0]
+      expect(notification.getType()).toBe 'info'
+
+    it "emits a success notification ::addSuccess has been called", ->
+      manager.addSuccess('Something!', icon: 'someIcon')
+      expect(addSpy).toHaveBeenCalled()
+      notification = addSpy.mostRecentCall.args[0]
+      expect(notification.getType()).toBe 'success'

spec/notification-spec.coffee

@@ -0,0 +1,18 @@
+Notification = require '../src/notification'
+
+describe "Notification", ->
+  [notification] = []
+
+  describe "::getTimestamp()", ->
+    it "returns a Date object", ->
+      notification = new Notification('error', 'message!')
+      expect(notification.getTimestamp() instanceof Date).toBe true
+
+  describe "::getIcon()", ->
+    it "returns a default when no icon specified", ->
+      notification = new Notification('error', 'message!')
+      expect(notification.getIcon()).toBe 'flame'
+
+    it "returns the icon specified", ->
+      notification = new Notification('error', 'message!', icon: 'my-icon')
+      expect(notification.getIcon()).toBe 'my-icon'

spec/package-manager-spec.coffee

@@ -2,8 +2,9 @@
 Package = require '../src/package'
 
 describe "PackageManager", ->
+  workspaceElement = null
   beforeEach ->
-    atom.workspaceView = atom.views.getView(atom.workspace).__spacePenView
+    workspaceElement = atom.views.getView(atom.workspace)
 
   describe "::loadPackage(name)", ->
     it "continues if the package has an invalid package.json", ->
@@ -111,7 +112,7 @@ describe "PackageManager", ->
           [mainModule, promise, workspaceCommandListener] = []
 
           beforeEach ->
-            atom.workspaceView.attachToDom()
+            jasmine.attachToDOM(workspaceElement)
             mainModule = require './fixtures/packages/package-with-activation-commands/index'
             mainModule.legacyActivationCommandCallCount = 0
             mainModule.activationCommandCallCount = 0
@@ -125,29 +126,29 @@ describe "PackageManager", ->
 
           it "defers requiring/activating the main module until an activation event bubbles to the root view", ->
             expect(promise.isFulfilled()).not.toBeTruthy()
-            atom.workspaceView[0].dispatchEvent(new CustomEvent('activation-command', bubbles: true))
+            workspaceElement.dispatchEvent(new CustomEvent('activation-command', bubbles: true))
 
             waitsForPromise ->
               promise
 
           it "triggers the activation event on all handlers registered during activation", ->
             waitsForPromise ->
-              atom.workspaceView.open()
+              atom.workspace.open()
 
             runs ->
-              editorView = atom.workspaceView.getActiveView()
+              editorView = atom.views.getView(atom.workspace.getActiveEditor()).__spacePenView
               legacyCommandListener = jasmine.createSpy("legacyCommandListener")
               editorView.command 'activation-command', legacyCommandListener
               editorCommandListener = jasmine.createSpy("editorCommandListener")
               atom.commands.add 'atom-text-editor', 'activation-command', editorCommandListener
-              editorView[0].dispatchEvent(new CustomEvent('activation-command', bubbles: true))
+              atom.commands.dispatch(editorView[0], 'activation-command')
               expect(mainModule.activate.callCount).toBe 1
               expect(mainModule.legacyActivationCommandCallCount).toBe 1
               expect(mainModule.activationCommandCallCount).toBe 1
               expect(legacyCommandListener.callCount).toBe 1
               expect(editorCommandListener.callCount).toBe 1
               expect(workspaceCommandListener.callCount).toBe 1
-              editorView[0].dispatchEvent(new CustomEvent('activation-command', bubbles: true))
+              atom.commands.dispatch(editorView[0], 'activation-command')
               expect(mainModule.legacyActivationCommandCallCount).toBe 2
               expect(mainModule.activationCommandCallCount).toBe 2
               expect(legacyCommandListener.callCount).toBe 2
@@ -349,8 +350,8 @@ describe "PackageManager", ->
             atom.packages.activatePackage('package-with-grammars')
 
           runs ->
-            expect(atom.syntax.selectGrammar('a.alot').name).toBe 'Alot'
-            expect(atom.syntax.selectGrammar('a.alittle').name).toBe 'Alittle'
+            expect(atom.grammars.selectGrammar('a.alot').name).toBe 'Alot'
+            expect(atom.grammars.selectGrammar('a.alittle').name).toBe 'Alittle'
 
       describe "scoped-property loading", ->
         it "loads the scoped properties", ->
@@ -362,13 +363,13 @@ describe "PackageManager", ->
 
     describe "converted textmate packages", ->
       it "loads the package's grammars", ->
-        expect(atom.syntax.selectGrammar("file.rb").name).toBe "Null Grammar"
+        expect(atom.grammars.selectGrammar("file.rb").name).toBe "Null Grammar"
 
         waitsForPromise ->
           atom.packages.activatePackage('language-ruby')
 
         runs ->
-          expect(atom.syntax.selectGrammar("file.rb").name).toBe "Ruby"
+          expect(atom.grammars.selectGrammar("file.rb").name).toBe "Ruby"
 
       it "loads the translated scoped properties", ->
         expect(atom.config.get(['.source.ruby'], 'editor.commentStart')).toBeUndefined()
@@ -454,8 +455,8 @@ describe "PackageManager", ->
 
         runs ->
           atom.packages.deactivatePackage('package-with-grammars')
-          expect(atom.syntax.selectGrammar('a.alot').name).toBe 'Null Grammar'
-          expect(atom.syntax.selectGrammar('a.alittle').name).toBe 'Null Grammar'
+          expect(atom.grammars.selectGrammar('a.alot').name).toBe 'Null Grammar'
+          expect(atom.grammars.selectGrammar('a.alittle').name).toBe 'Null Grammar'
 
       it "removes the package's keymaps", ->
         waitsForPromise ->
@@ -490,15 +491,15 @@ describe "PackageManager", ->
 
     describe "textmate packages", ->
       it "removes the package's grammars", ->
-        expect(atom.syntax.selectGrammar("file.rb").name).toBe "Null Grammar"
+        expect(atom.grammars.selectGrammar("file.rb").name).toBe "Null Grammar"
 
         waitsForPromise ->
           atom.packages.activatePackage('language-ruby')
 
         runs ->
-          expect(atom.syntax.selectGrammar("file.rb").name).toBe "Ruby"
+          expect(atom.grammars.selectGrammar("file.rb").name).toBe "Ruby"
           atom.packages.deactivatePackage('language-ruby')
-          expect(atom.syntax.selectGrammar("file.rb").name).toBe "Null Grammar"
+          expect(atom.grammars.selectGrammar("file.rb").name).toBe "Null Grammar"
 
       it "removes the package's scoped properties", ->
         waitsForPromise ->
@@ -526,8 +527,8 @@ describe "PackageManager", ->
       atom.packages.deactivatePackages()
       atom.packages.unloadPackages()
 
-      Syntax = require '../src/syntax'
-      atom.syntax = window.syntax = new Syntax()
+      GrammarRegistry = require '../src/grammar-registry'
+      atom.grammars = window.syntax = new GrammarRegistry()
 
     it "activates all the packages, and none of the themes", ->
       atom.packages.activate()

spec/panel-container-element-spec.coffee

@@ -43,6 +43,19 @@ describe "PanelContainerElement", ->
     expect(element.parentNode).not.toBe jasmineContent
 
   describe "adding and removing panels", ->
+    it "allows panels to be inserted at any position", ->
+      panel1 = new Panel({viewRegistry, item: new TestPanelContainerItem(), priority: 10})
+      panel2 = new Panel({viewRegistry, item: new TestPanelContainerItem(), priority: 5})
+      panel3 = new Panel({viewRegistry, item: new TestPanelContainerItem(), priority: 8})
+
+      container.addPanel(panel1)
+      container.addPanel(panel2)
+      container.addPanel(panel3)
+
+      expect(element.childNodes[2].getModel()).toBe(panel1)
+      expect(element.childNodes[1].getModel()).toBe(panel3)
+      expect(element.childNodes[0].getModel()).toBe(panel2)
+
     describe "when the container is at the left location", ->
       it "adds atom-panel elements when a new panel is added to the container; removes them when the panels are destroyed", ->
         expect(element.childNodes.length).toBe 0
@@ -51,6 +64,8 @@ describe "PanelContainerElement", ->
         container.addPanel(panel1)
         expect(element.childNodes.length).toBe 1
         expect(element.childNodes[0]).toHaveClass 'left'
+        expect(element.childNodes[0]).toHaveClass 'tool-panel' # legacy selector support
+        expect(element.childNodes[0]).toHaveClass 'panel-left' # legacy selector support
 
         expect(element.childNodes[0].tagName).toBe 'ATOM-PANEL'
 
@@ -80,6 +95,8 @@ describe "PanelContainerElement", ->
         container.addPanel(panel1)
         expect(element.childNodes.length).toBe 1
         expect(element.childNodes[0]).toHaveClass 'bottom'
+        expect(element.childNodes[0]).toHaveClass 'tool-panel' # legacy selector support
+        expect(element.childNodes[0]).toHaveClass 'panel-bottom' # legacy selector support
         expect(element.childNodes[0].tagName).toBe 'ATOM-PANEL'
         expect(panel1.getView()).toHaveClass 'one'
 
@@ -116,3 +133,14 @@ describe "PanelContainerElement", ->
 
       expect(panel1.getView().style.display).not.toBe 'none'
       expect(panel2.getView().style.display).toBe 'none'
+
+    it "adds the 'modal' class to panels", ->
+      panel1 = new Panel({viewRegistry, item: new TestPanelContainerItem()})
+      container.addPanel(panel1)
+
+      expect(panel1.getView()).toHaveClass 'modal'
+
+      # legacy selector support
+      expect(panel1.getView()).not.toHaveClass 'tool-panel'
+      expect(panel1.getView()).toHaveClass 'overlay'
+      expect(panel1.getView()).toHaveClass 'from-top'

spec/spec-helper.coffee

@@ -9,7 +9,8 @@ _ = require 'underscore-plus'
 fs = require 'fs-plus'
 Grim = require 'grim'
 KeymapManager = require '../src/keymap-extensions'
-{$, WorkspaceView, Workspace} = require 'atom'
+Workspace = require '../src/workspace'
+{$} = require '../src/space-pen-extensions'
 Config = require '../src/config'
 {Point} = require 'text-buffer'
 Project = require '../src/project'
@@ -82,7 +83,7 @@ beforeEach ->
   serializedWindowState = null
 
   spyOn(atom, 'saveSync')
-  atom.syntax.clearGrammarOverrides()
+  atom.grammars.clearGrammarOverrides()
 
   spy = spyOn(atom.packages, 'resolvePackagePath').andCallFake (packageName) ->
     if specPackageName and packageName is specPackageName
@@ -135,8 +136,9 @@ afterEach ->
   atom.menu.template = []
   atom.contextMenu.clear()
 
-  atom.workspaceView?.remove?()
-  atom.workspaceView = null
+  atom.workspace?.destroy()
+  atom.workspace = null
+  atom.__workspaceView = null
   delete atom.state.workspace
 
   atom.project?.destroy()
@@ -150,7 +152,7 @@ afterEach ->
 
   jasmine.unspy(atom, 'saveSync')
   ensureNoPathSubscriptions()
-  atom.syntax.clearObservers()
+  atom.grammars.clearObservers()
   waits(0) # yield to ui thread to make screen update more frequently
 
 ensureNoPathSubscriptions = ->
@@ -191,6 +193,10 @@ jasmine.unspy = (object, methodName) ->
   throw new Error("Not a spy") unless object[methodName].hasOwnProperty('originalValue')
   object[methodName] = object[methodName].originalValue
 
+jasmine.attachToDOM = (element) ->
+  jasmineContent = document.querySelector('#jasmine-content')
+  jasmineContent.appendChild(element) unless jasmineContent.contains(element)
+
 addCustomMatchers = (spec) ->
   spec.addMatchers
     toBeInstanceOf: (expected) ->

spec/syntax-spec.coffee

@@ -23,10 +23,10 @@ describe "the `syntax` global", ->
   describe "serialization", ->
     it "remembers grammar overrides by path", ->
       filePath = '/foo/bar/file.js'
-      expect(atom.syntax.selectGrammar(filePath).name).not.toBe 'Ruby'
-      atom.syntax.setGrammarOverrideForPath(filePath, 'source.ruby')
-      syntax2 = atom.deserializers.deserialize(atom.syntax.serialize())
-      syntax2.addGrammar(grammar) for grammar in atom.syntax.grammars when grammar isnt atom.syntax.nullGrammar
+      expect(atom.grammars.selectGrammar(filePath).name).not.toBe 'Ruby'
+      atom.grammars.setGrammarOverrideForPath(filePath, 'source.ruby')
+      syntax2 = atom.deserializers.deserialize(atom.grammars.serialize())
+      syntax2.addGrammar(grammar) for grammar in atom.grammars.grammars when grammar isnt atom.grammars.nullGrammar
       expect(syntax2.selectGrammar(filePath).name).toBe 'Ruby'
 
   describe ".selectGrammar(filePath)", ->
@@ -35,15 +35,15 @@ describe "the `syntax` global", ->
         atom.packages.activatePackage('language-git')
 
       runs ->
-        expect(atom.syntax.selectGrammar("file.js").name).toBe "JavaScript" # based on extension (.js)
-        expect(atom.syntax.selectGrammar(path.join(temp.dir, '.git', 'config')).name).toBe "Git Config" # based on end of the path (.git/config)
-        expect(atom.syntax.selectGrammar("Rakefile").name).toBe "Ruby" # based on the file's basename (Rakefile)
-        expect(atom.syntax.selectGrammar("curb").name).toBe "Null Grammar"
-        expect(atom.syntax.selectGrammar("/hu.git/config").name).toBe "Null Grammar"
+        expect(atom.grammars.selectGrammar("file.js").name).toBe "JavaScript" # based on extension (.js)
+        expect(atom.grammars.selectGrammar(path.join(temp.dir, '.git', 'config')).name).toBe "Git Config" # based on end of the path (.git/config)
+        expect(atom.grammars.selectGrammar("Rakefile").name).toBe "Ruby" # based on the file's basename (Rakefile)
+        expect(atom.grammars.selectGrammar("curb").name).toBe "Null Grammar"
+        expect(atom.grammars.selectGrammar("/hu.git/config").name).toBe "Null Grammar"
 
     it "uses the filePath's shebang line if the grammar cannot be determined by the extension or basename", ->
       filePath = require.resolve("./fixtures/shebang")
-      expect(atom.syntax.selectGrammar(filePath).name).toBe "Ruby"
+      expect(atom.grammars.selectGrammar(filePath).name).toBe "Ruby"
 
     it "uses the number of newlines in the first line regex to determine the number of lines to test against", ->
       waitsForPromise ->
@@ -51,28 +51,28 @@ describe "the `syntax` global", ->
 
       runs ->
         fileContent = "first-line\n<html>"
-        expect(atom.syntax.selectGrammar("dummy.coffee", fileContent).name).toBe "CoffeeScript"
+        expect(atom.grammars.selectGrammar("dummy.coffee", fileContent).name).toBe "CoffeeScript"
 
         fileContent = '<?xml version="1.0" encoding="UTF-8"?>'
-        expect(atom.syntax.selectGrammar("grammar.tmLanguage", fileContent).name).toBe "Null Grammar"
+        expect(atom.grammars.selectGrammar("grammar.tmLanguage", fileContent).name).toBe "Null Grammar"
 
         fileContent += '\n<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">'
-        expect(atom.syntax.selectGrammar("grammar.tmLanguage", fileContent).name).toBe "Property List (XML)"
+        expect(atom.grammars.selectGrammar("grammar.tmLanguage", fileContent).name).toBe "Property List (XML)"
 
     it "doesn't read the file when the file contents are specified", ->
       filePath = require.resolve("./fixtures/shebang")
       filePathContents = fs.readFileSync(filePath, 'utf8')
       spyOn(fs, 'read').andCallThrough()
-      expect(atom.syntax.selectGrammar(filePath, filePathContents).name).toBe "Ruby"
+      expect(atom.grammars.selectGrammar(filePath, filePathContents).name).toBe "Ruby"
       expect(fs.read).not.toHaveBeenCalled()
 
     it "allows the default grammar to be overridden for a path", ->
       filePath = '/foo/bar/file.js'
-      expect(atom.syntax.selectGrammar(filePath).name).not.toBe 'Ruby'
-      atom.syntax.setGrammarOverrideForPath(filePath, 'source.ruby')
-      expect(atom.syntax.selectGrammar(filePath).name).toBe 'Ruby'
-      atom.syntax.clearGrammarOverrideForPath(filePath)
-      expect(atom.syntax.selectGrammar(filePath).name).not.toBe 'Ruby'
+      expect(atom.grammars.selectGrammar(filePath).name).not.toBe 'Ruby'
+      atom.grammars.setGrammarOverrideForPath(filePath, 'source.ruby')
+      expect(atom.grammars.selectGrammar(filePath).name).toBe 'Ruby'
+      atom.grammars.clearGrammarOverrideForPath(filePath)
+      expect(atom.grammars.selectGrammar(filePath).name).not.toBe 'Ruby'
 
     describe "when multiple grammars have matching fileTypes", ->
       it "selects the grammar with the longest fileType match", ->
@@ -82,8 +82,8 @@ describe "the `syntax` global", ->
           scopeName: 'source1'
           fileTypes: ['test']
         )
-        grammar1 = atom.syntax.loadGrammarSync(grammarPath1)
-        expect(atom.syntax.selectGrammar('more.test', '')).toBe grammar1
+        grammar1 = atom.grammars.loadGrammarSync(grammarPath1)
+        expect(atom.grammars.selectGrammar('more.test', '')).toBe grammar1
 
         grammarPath2 = temp.path(suffix: '.json')
         fs.writeFileSync grammarPath2, JSON.stringify(
@@ -91,44 +91,44 @@ describe "the `syntax` global", ->
           scopeName: 'source2'
           fileTypes: ['test', 'more.test']
         )
-        grammar2 = atom.syntax.loadGrammarSync(grammarPath2)
-        expect(atom.syntax.selectGrammar('more.test', '')).toBe grammar2
+        grammar2 = atom.grammars.loadGrammarSync(grammarPath2)
+        expect(atom.grammars.selectGrammar('more.test', '')).toBe grammar2
 
     describe "when there is no file path", ->
       it "does not throw an exception (regression)", ->
-        expect(-> atom.syntax.selectGrammar(null, '#!/usr/bin/ruby')).not.toThrow()
-        expect(-> atom.syntax.selectGrammar(null, '')).not.toThrow()
-        expect(-> atom.syntax.selectGrammar(null, null)).not.toThrow()
+        expect(-> atom.grammars.selectGrammar(null, '#!/usr/bin/ruby')).not.toThrow()
+        expect(-> atom.grammars.selectGrammar(null, '')).not.toThrow()
+        expect(-> atom.grammars.selectGrammar(null, null)).not.toThrow()
 
   describe ".removeGrammar(grammar)", ->
     it "removes the grammar, so it won't be returned by selectGrammar", ->
-      grammar = atom.syntax.selectGrammar('foo.js')
-      atom.syntax.removeGrammar(grammar)
-      expect(atom.syntax.selectGrammar('foo.js').name).not.toBe grammar.name
+      grammar = atom.grammars.selectGrammar('foo.js')
+      atom.grammars.removeGrammar(grammar)
+      expect(atom.grammars.selectGrammar('foo.js').name).not.toBe grammar.name
 
   describe ".getProperty(scopeDescriptor)", ->
     it "returns the property with the most specific scope selector", ->
-      atom.syntax.addProperties(".source.coffee .string.quoted.double.coffee", foo: bar: baz: 42)
-      atom.syntax.addProperties(".source .string.quoted.double", foo: bar: baz: 22)
-      atom.syntax.addProperties(".source", foo: bar: baz: 11)
+      atom.grammars.addProperties(".source.coffee .string.quoted.double.coffee", foo: bar: baz: 42)
+      atom.grammars.addProperties(".source .string.quoted.double", foo: bar: baz: 22)
+      atom.grammars.addProperties(".source", foo: bar: baz: 11)
 
-      expect(atom.syntax.getProperty([".source.coffee", ".string.quoted.double.coffee"], "foo.bar.baz")).toBe 42
-      expect(atom.syntax.getProperty([".source.js", ".string.quoted.double.js"], "foo.bar.baz")).toBe 22
-      expect(atom.syntax.getProperty([".source.js", ".variable.assignment.js"], "foo.bar.baz")).toBe 11
-      expect(atom.syntax.getProperty([".text"], "foo.bar.baz")).toBeUndefined()
+      expect(atom.grammars.getProperty([".source.coffee", ".string.quoted.double.coffee"], "foo.bar.baz")).toBe 42
+      expect(atom.grammars.getProperty([".source.js", ".string.quoted.double.js"], "foo.bar.baz")).toBe 22
+      expect(atom.grammars.getProperty([".source.js", ".variable.assignment.js"], "foo.bar.baz")).toBe 11
+      expect(atom.grammars.getProperty([".text"], "foo.bar.baz")).toBeUndefined()
 
     it "favors the most recently added properties in the event of a specificity tie", ->
-      atom.syntax.addProperties(".source.coffee .string.quoted.single", foo: bar: baz: 42)
-      atom.syntax.addProperties(".source.coffee .string.quoted.double", foo: bar: baz: 22)
+      atom.grammars.addProperties(".source.coffee .string.quoted.single", foo: bar: baz: 42)
+      atom.grammars.addProperties(".source.coffee .string.quoted.double", foo: bar: baz: 22)
 
-      expect(atom.syntax.getProperty([".source.coffee", ".string.quoted.single"], "foo.bar.baz")).toBe 42
-      expect(atom.syntax.getProperty([".source.coffee", ".string.quoted.single.double"], "foo.bar.baz")).toBe 22
+      expect(atom.grammars.getProperty([".source.coffee", ".string.quoted.single"], "foo.bar.baz")).toBe 42
+      expect(atom.grammars.getProperty([".source.coffee", ".string.quoted.single.double"], "foo.bar.baz")).toBe 22
 
   describe ".removeProperties(name)", ->
     it "allows properties to be removed by name", ->
-      atom.syntax.addProperties("a", ".source.coffee .string.quoted.double.coffee", foo: bar: baz: 42)
-      atom.syntax.addProperties("b", ".source .string.quoted.double", foo: bar: baz: 22)
+      atom.grammars.addProperties("a", ".source.coffee .string.quoted.double.coffee", foo: bar: baz: 42)
+      atom.grammars.addProperties("b", ".source .string.quoted.double", foo: bar: baz: 22)
 
-      atom.syntax.removeProperties("b")
-      expect(atom.syntax.getProperty([".source.js", ".string.quoted.double.js"], "foo.bar.baz")).toBeUndefined()
-      expect(atom.syntax.getProperty([".source.coffee", ".string.quoted.double.coffee"], "foo.bar.baz")).toBe 42
+      atom.grammars.removeProperties("b")
+      expect(atom.grammars.getProperty([".source.js", ".string.quoted.double.js"], "foo.bar.baz")).toBeUndefined()
+      expect(atom.grammars.getProperty([".source.coffee", ".string.quoted.double.coffee"], "foo.bar.baz")).toBe 42

spec/text-editor-component-spec.coffee

@@ -2532,7 +2532,7 @@ describe "TextEditorComponent", ->
   describe "grammar data attributes", ->
     it "adds and updates the grammar data attribute based on the current grammar", ->
       expect(wrapperNode.dataset.grammar).toBe 'source js'
-      editor.setGrammar(atom.syntax.nullGrammar)
+      editor.setGrammar(atom.grammars.nullGrammar)
       expect(wrapperNode.dataset.grammar).toBe 'text plain null-grammar'
 
   describe "encoding data attributes", ->

spec/text-editor-spec.coffee

@@ -2607,69 +2607,44 @@ describe "TextEditor", ->
               atom.clipboard.write(" z();")
               editor.setCursorBufferPosition([1, Infinity])
               editor.pasteText()
-
-              console.log JSON.stringify(editor.lineTextForBufferRow(1))
               expect(editor.lineTextForBufferRow(1)).toBe("    y(); z();")
 
         describe "when `autoIndentOnPaste` is false", ->
           beforeEach ->
             atom.config.set('editor.autoIndentOnPaste', false)
 
-          describe "when the inserted text contains no newlines", ->
-            it "does not adjust the indentation level of the text", ->
-              editor.setCursorBufferPosition([5, 2])
-              editor.insertText("foo", indentBasis: 5)
-              expect(editor.lineTextForBufferRow(5)).toBe "  foo    current = items.shift();"
+          describe "when the cursor is indented further than the original copied text", ->
+            it "increases the indentation of the copied lines to match", ->
+              editor.setSelectedBufferRange([[1, 2], [3, 0]])
+              editor.copySelectedText()
 
-            it "does not adjust the whitespace if there are preceding characters", ->
-              copyText(" foo")
-              editor.setCursorBufferPosition([5, 30])
+              editor.setCursorBufferPosition([5, 6])
               editor.pasteText()
 
-              expect(editor.lineTextForBufferRow(5)).toBe "      current = items.shift(); foo"
+              expect(editor.lineTextForBufferRow(5)).toBe "      var sort = function(items) {"
+              expect(editor.lineTextForBufferRow(6)).toBe "        if (items.length <= 1) return items;"
 
-          describe "when the inserted text contains newlines", ->
-            describe "when the cursor is preceded only by whitespace characters", ->
-              it "normalizes indented lines to each cursor's current indentation level", ->
-                editor.setSelectedBufferRanges([
-                  [[1,2], [3,0]],
-                  [[4,4], [6,0]]
-                ])
-                editor.copySelectedText()
-                expect(atom.clipboard.read()).toEqual """
-                  var sort = function(items) {
-                      if (items.length <= 1) return items;
+          describe "when the cursor is indented less far than the original copied text", ->
+            it "decreases the indentation of the copied lines to match", ->
+              editor.setSelectedBufferRange([[6, 6], [8, 0]])
+              editor.copySelectedText()
 
-                  while(items.length > 0) {
-                        current = items.shift();
+              editor.setCursorBufferPosition([1, 2])
+              editor.pasteText()
 
-                """
+              expect(editor.lineTextForBufferRow(1)).toBe "  current < pivot ? left.push(current) : right.push(current);"
+              expect(editor.lineTextForBufferRow(2)).toBe "}"
 
-                editor.setCursorBufferPosition([0,0])
-                editor.insertNewlineAbove()
-                editor.setSelectedBufferRanges([
-                  [[0,0], [0,0]],
-                  [[1,0], [1,0]]
-                ])
-                editor.pasteText()
+          describe "when the first copied line has leading whitespace", ->
+            it "preserves the line's leading whitespace", ->
+              editor.setSelectedBufferRange([[4, 0], [6, 0]])
+              editor.copySelectedText()
 
-                expect(editor.lineTextForBufferRow(0)).toBe "var sort = function(items) {"
-                console.log JSON.stringify(editor.lineTextForBufferRow(1))
-                expect(editor.lineTextForBufferRow(1)).toBe "  if (items.length <= 1) return items;"
-                expect(editor.lineTextForBufferRow(2)).toBe ""
-                expect(editor.lineTextForBufferRow(3)).toBe "while(items.length > 0) {"
-                expect(editor.lineTextForBufferRow(4)).toBe "  current = items.shift();"
+              editor.setCursorBufferPosition([0, 0])
+              editor.pasteText()
 
-            describe "when the cursor is preceded by non-whitespace characters", ->
-              it "normalizes the indentation level of all lines based on the level of the existing first line", ->
-                copyText("    while (true) {\n      foo();\n    }\n", {startColumn: 0})
-                editor.setCursorBufferPosition([1, Infinity])
-                editor.pasteText()
-
-                expect(editor.lineTextForBufferRow(1)).toBe "  var sort = function(items) {while (true) {"
-                expect(editor.lineTextForBufferRow(2)).toBe "    foo();"
-                expect(editor.lineTextForBufferRow(3)).toBe "  }"
-                expect(editor.lineTextForBufferRow(4)).toBe ""
+              expect(editor.lineTextForBufferRow(0)).toBe "    while(items.length > 0) {"
+              expect(editor.lineTextForBufferRow(1)).toBe "      current = items.shift();"
 
         describe 'when the clipboard has many selections', ->
           beforeEach ->
@@ -3357,17 +3332,17 @@ describe "TextEditor", ->
     it "switches to the better-matched grammar and re-tokenizes the buffer", ->
       editor.destroy()
 
-      jsGrammar = atom.syntax.selectGrammar('a.js')
-      atom.syntax.removeGrammar(jsGrammar)
+      jsGrammar = atom.grammars.selectGrammar('a.js')
+      atom.grammars.removeGrammar(jsGrammar)
 
       waitsForPromise ->
         atom.workspace.open('sample.js', autoIndent: false).then (o) -> editor = o
 
       runs ->
-        expect(editor.getGrammar()).toBe atom.syntax.nullGrammar
+        expect(editor.getGrammar()).toBe atom.grammars.nullGrammar
         expect(editor.tokenizedLineForScreenRow(0).tokens.length).toBe 1
 
-        atom.syntax.addGrammar(jsGrammar)
+        atom.grammars.addGrammar(jsGrammar)
         expect(editor.getGrammar()).toBe jsGrammar
         expect(editor.tokenizedLineForScreenRow(0).tokens.length).toBeGreaterThan 1
 
@@ -3787,7 +3762,7 @@ describe "TextEditor", ->
 
     it "updates the grammar based on grammar overrides", ->
       expect(editor.getGrammar().name).toBe 'JavaScript'
-      atom.syntax.setGrammarOverrideForPath(editor.getPath(), 'source.coffee')
+      atom.grammars.setGrammarOverrideForPath(editor.getPath(), 'source.coffee')
       editor.reloadGrammar()
       expect(editor.getGrammar().name).toBe 'CoffeeScript'
 
@@ -3805,7 +3780,7 @@ describe "TextEditor", ->
         atom.packages.activatePackage('language-hyperlink')
 
       runs ->
-        grammar = atom.syntax.selectGrammar("text.js")
+        grammar = atom.grammars.selectGrammar("text.js")
         {tokens} = grammar.tokenizeLine("var i; // http://github.com")
 
         expect(tokens[0].value).toBe "var"

spec/theme-manager-spec.coffee

@@ -207,10 +207,11 @@ describe "ThemeManager", ->
       expect(stylesheetsChangedHandler).toHaveBeenCalled()
 
   describe "base stylesheet loading", ->
+    workspaceElement = null
     beforeEach ->
-      atom.workspaceView = atom.views.getView(atom.workspace).__spacePenView
-      atom.workspaceView.append $('<atom-text-editor>')
-      atom.workspaceView.attachToDom()
+      workspaceElement = atom.views.getView(atom.workspace)
+      jasmine.attachToDOM(workspaceElement)
+      workspaceElement.appendChild document.createElement('atom-text-editor')
 
       waitsForPromise ->
         themeManager.activateThemes()
@@ -224,7 +225,7 @@ describe "ThemeManager", ->
 
       runs ->
         # an override loaded in the base css
-        expect(atom.workspaceView.css("background-color")).toBe "rgb(0, 0, 255)"
+        expect(getComputedStyle(workspaceElement)["background-color"]).toBe "rgb(0, 0, 255)"
 
         # from within the theme itself
         expect($("atom-text-editor").css("padding-top")).toBe "150px"
@@ -241,14 +242,14 @@ describe "ThemeManager", ->
 
         runs ->
           # an override loaded in the base css
-          expect(atom.workspaceView.css("background-color")).toBe "rgb(0, 0, 255)"
+          expect(getComputedStyle(workspaceElement)["background-color"]).toBe "rgb(0, 0, 255)"
 
           # from within the theme itself
           expect($("atom-text-editor").css("background-color")).toBe "rgb(0, 152, 255)"
 
     describe "theme classes on the workspace", ->
       it 'adds theme-* classes to the workspace for each active theme', ->
-        expect(atom.workspaceView).toHaveClass 'theme-atom-dark-ui'
+        expect(workspaceElement).toHaveClass 'theme-atom-dark-ui'
 
         themeManager.onDidReloadAll reloadHandler = jasmine.createSpy()
         atom.config.set('core.themes', ['theme-with-ui-variables', 'theme-with-syntax-variables'])
@@ -258,10 +259,10 @@ describe "ThemeManager", ->
 
         runs ->
           # `theme-` twice as it prefixes the name with `theme-`
-          expect(atom.workspaceView).toHaveClass 'theme-theme-with-ui-variables'
-          expect(atom.workspaceView).toHaveClass 'theme-theme-with-syntax-variables'
-          expect(atom.workspaceView).not.toHaveClass 'theme-atom-dark-ui'
-          expect(atom.workspaceView).not.toHaveClass 'theme-atom-dark-syntax'
+          expect(workspaceElement).toHaveClass 'theme-theme-with-ui-variables'
+          expect(workspaceElement).toHaveClass 'theme-theme-with-syntax-variables'
+          expect(workspaceElement).not.toHaveClass 'theme-atom-dark-ui'
+          expect(workspaceElement).not.toHaveClass 'theme-atom-dark-syntax'
 
   describe "when the user stylesheet changes", ->
     it "reloads it", ->

spec/tokenized-buffer-spec.coffee

@@ -522,7 +522,7 @@ describe "TokenizedBuffer", ->
         buffer = atom.project.bufferForPathSync()
         buffer.setText "<div class='name'><%= User.find(2).full_name %></div>"
         tokenizedBuffer = new TokenizedBuffer({buffer})
-        tokenizedBuffer.setGrammar(atom.syntax.selectGrammar('test.erb'))
+        tokenizedBuffer.setGrammar(atom.grammars.selectGrammar('test.erb'))
         fullyTokenize(tokenizedBuffer)
 
         {tokens} = tokenizedBuffer.tokenizedLineForRow(0)

spec/tooltip-manager-spec.coffee

@@ -0,0 +1,72 @@
+TooltipManager = require '../src/tooltip-manager'
+{$} = require '../src/space-pen-extensions'
+
+describe "TooltipManager", ->
+  [manager, element] = []
+
+  beforeEach ->
+    manager = new TooltipManager
+    element = document.createElement('div')
+    element.classList.add('foo')
+    jasmine.attachToDOM(element)
+
+  hover = (element, fn) ->
+    $(element).trigger 'mouseenter'
+    advanceClock(manager.defaults.delay.show)
+    fn()
+    $(element).trigger 'mouseleave'
+    advanceClock(manager.defaults.delay.hide)
+
+  describe "::add(target, options)", ->
+    describe "when the target is an element", ->
+      it "creates a tooltip based on the given options when hovering over the target element", ->
+        manager.add element, title: "Title"
+        hover element, ->
+          expect(document.body.querySelector(".tooltip")).toHaveText("Title")
+
+    describe "when a keyBindingCommand is specified", ->
+      describe "when a title is specified", ->
+        it "appends the key binding corresponding to the command to the title", ->
+          atom.keymaps.add 'test',
+            '.foo': 'ctrl-x ctrl-y': 'test-command'
+            '.bar': 'ctrl-x ctrl-z': 'test-command'
+
+          manager.add element, title: "Title", keyBindingCommand: 'test-command'
+
+          hover element, ->
+            tooltipElement = document.body.querySelector(".tooltip")
+            expect(tooltipElement).toHaveText "Title ⌃X ⌃Y"
+
+      describe "when no title is specified", ->
+        it "shows the key binding corresponding to the command alone", ->
+          atom.keymaps.add 'test', '.foo': 'ctrl-x ctrl-y': 'test-command'
+
+          manager.add element, keyBindingCommand: 'test-command'
+
+          hover element, ->
+            tooltipElement = document.body.querySelector(".tooltip")
+            expect(tooltipElement).toHaveText "⌃X ⌃Y"
+
+      describe "when a keyBindingTarget is specified", ->
+        it "looks up the key binding relative to the target", ->
+          atom.keymaps.add 'test',
+            '.bar': 'ctrl-x ctrl-z': 'test-command'
+            '.foo': 'ctrl-x ctrl-y': 'test-command'
+
+          manager.add element, keyBindingCommand: 'test-command', keyBindingTarget: element
+
+          hover element, ->
+            tooltipElement = document.body.querySelector(".tooltip")
+            expect(tooltipElement).toHaveText "⌃X ⌃Y"
+
+    describe "when .dispose() is called on the returned disposable", ->
+      it "no longer displays the tooltip on hover", ->
+        disposable = manager.add element, title: "Title"
+
+        hover element, ->
+          expect(document.body.querySelector(".tooltip")).toHaveText("Title")
+
+        disposable.dispose()
+
+        hover element, ->
+          expect(document.body.querySelector(".tooltip")).toBeNull()

spec/window-spec.coffee

@@ -95,13 +95,13 @@ describe "Window", ->
   describe ".unloadEditorWindow()", ->
     it "saves the serialized state of the window so it can be deserialized after reload", ->
       workspaceState = atom.workspace.serialize()
-      syntaxState = atom.syntax.serialize()
+      syntaxState = atom.grammars.serialize()
       projectState = atom.project.serialize()
 
       atom.unloadEditorWindow()
 
       expect(atom.state.workspace).toEqual workspaceState
-      expect(atom.state.syntax).toEqual syntaxState
+      expect(atom.state.grammars).toEqual syntaxState
       expect(atom.state.project).toEqual projectState
       expect(atom.saveSync).toHaveBeenCalled()
 
@@ -112,9 +112,9 @@ describe "Window", ->
 
       runs ->
         buffer = atom.workspace.getActivePaneItem().buffer
-        pane = atom.workspaceView.getActivePaneView()
-        pane.splitRight(pane.copyActiveItem())
-        expect(atom.workspaceView.find('atom-text-editor').length).toBe 2
+        pane = atom.workspace.getActivePane()
+        pane.splitRight(copyActiveItem: true)
+        expect(atom.workspace.getTextEditors().length).toBe 2
 
         atom.removeEditorWindow()
 

spec/workspace-spec.coffee

@@ -500,4 +500,3 @@ describe "Workspace", ->
 
         expect(panel).toBeDefined()
         expect(addPanelSpy).toHaveBeenCalledWith({panel, index: 0})
-        expect(panel.getClassName()).toBe 'overlay from-top' # the default

src/atom.coffee

@@ -5,6 +5,7 @@ path = require 'path'
 remote = require 'remote'
 screen = require 'screen'
 shell = require 'shell'
+{deprecate} = require 'grim'
 
 _ = require 'underscore-plus'
 {deprecate} = require 'grim'
@@ -33,6 +34,23 @@ class Atom extends Model
     startTime = Date.now()
     atom = @deserialize(@loadState(mode)) ? new this({mode, @version})
     atom.deserializeTimings.atom = Date.now() -  startTime
+
+    workspaceViewDeprecationMessage = """
+      atom.workspaceView is no longer available.
+      In most cases you will not need the view. See the Workspace docs for
+      alternatives: https://atom.io/docs/api/latest/Workspace.
+      If you do need the view, please use `atom.views.getView(atom.workspace)`,
+      which returns an HTMLElement.
+    """
+
+    Object.defineProperty atom, 'workspaceView',
+      get: ->
+        deprecate(workspaceViewDeprecationMessage)
+        atom.__workspaceView
+      set: (newValue) ->
+        deprecate(workspaceViewDeprecationMessage)
+        atom.__workspaceView = newValue
+
     atom
 
   # Deserializes the Atom environment from a state object
@@ -125,11 +143,17 @@ class Atom extends Model
   # Public: A {KeymapManager} instance
   keymaps: null
 
+  # Public: A {TooltipManager} instance
+  tooltips: null
+
+  # Experimental: A {NotificationManager} instance
+  notifications: null
+
   # Public: A {Project} instance
   project: null
 
-  # Public: A {Syntax} instance
-  syntax: null
+  # Public: A {GrammarRegistry} instance
+  grammars: null
 
   # Public: A {PackageManager} instance
   packages: null
@@ -149,9 +173,6 @@ class Atom extends Model
   # Public: A {Workspace} instance
   workspace: null
 
-  # Public: A {WorkspaceView} instance
-  workspaceView: null
-
   ###
   Section: Construction and Destruction
   ###
@@ -201,9 +222,11 @@ class Atom extends Model
     KeymapManager = require './keymap-extensions'
     ViewRegistry = require './view-registry'
     CommandRegistry = require './command-registry'
+    TooltipManager = require './tooltip-manager'
+    NotificationManager = require './notification-manager'
     PackageManager = require './package-manager'
     Clipboard = require './clipboard'
-    Syntax = require './syntax'
+    GrammarRegistry = require './grammar-registry'
     ThemeManager = require './theme-manager'
     StyleManager = require './style-manager'
     ContextMenuManager = require './context-menu-manager'
@@ -226,6 +249,9 @@ class Atom extends Model
     @config = new Config({configDirPath, resourcePath})
     @keymaps = new KeymapManager({configDirPath, resourcePath})
     @keymap = @keymaps # Deprecated
+    @keymaps.subscribeToFileReadFailure()
+    @tooltips = new TooltipManager
+    @notifications = new NotificationManager
     @commands = new CommandRegistry
     @views = new ViewRegistry
     @packages = new PackageManager({devMode, configDirPath, resourcePath, safeMode})
@@ -236,7 +262,11 @@ class Atom extends Model
     @menu = new MenuManager({resourcePath})
     @clipboard = new Clipboard()
 
-    @syntax = @deserializers.deserialize(@state.syntax) ? new Syntax()
+    @grammars = @deserializers.deserialize(@state.grammars ? @state.syntax) ? new GrammarRegistry()
+
+    Object.defineProperty this, 'syntax', get: ->
+      deprecate "The atom.syntax global is deprecated. Use atom.grammars instead."
+      @grammars
 
     @subscribe @packages.onDidActivateAll => @watchThemes()
 
@@ -547,9 +577,9 @@ class Atom extends Model
     @displayWindow({maximize})
 
   unloadEditorWindow: ->
-    return if not @project and not @workspaceView
+    return if not @project
 
-    @state.syntax = @syntax.serialize()
+    @state.grammars = @grammars.serialize()
     @state.project = @project.serialize()
     @state.workspace = @workspace.serialize()
     @packages.deactivatePackages()
@@ -558,10 +588,10 @@ class Atom extends Model
     @windowState = null
 
   removeEditorWindow: ->
-    return if not @project and not @workspaceView
+    return if not @project
 
-    @workspaceView?.remove()
-    @workspaceView = null
+    @workspace?.destroy()
+    @workspace = null
     @project?.destroy()
     @project = null
 
@@ -574,7 +604,7 @@ class Atom extends Model
   # Essential: Visually and audibly trigger a beep.
   beep: ->
     shell.beep() if @config.get('core.audioBeep')
-    @workspaceView.trigger 'beep'
+    @__workspaceView.trigger 'beep'
     @emitter.emit 'did-beep'
 
   # Essential: A flexible way to open a dialog akin to an alert dialog.
@@ -650,11 +680,13 @@ class Atom extends Model
 
     startTime = Date.now()
     @workspace = Workspace.deserialize(@state.workspace) ? new Workspace
-    @workspaceView = @views.getView(@workspace).__spacePenView
+
+    workspaceElement = @views.getView(@workspace)
+    @__workspaceView = workspaceElement.__spacePenView
     @deserializeTimings.workspace = Date.now() - startTime
 
-    @keymaps.defaultTarget = @workspaceView[0]
-    $(@workspaceViewParentSelector).append(@workspaceView)
+    @keymaps.defaultTarget = workspaceElement
+    document.querySelector(@workspaceViewParentSelector).appendChild(workspaceElement)
 
   deserializePackageStates: ->
     @packages.packageStates = @state.packageStates ? {}

src/browser/main.coffee

@@ -13,6 +13,16 @@ process.on 'uncaughtException', (error={}) ->
   nslog(error.message) if error.message?
   nslog(error.stack) if error.stack?
 
+# Patch fs.statSyncNoException/fs.lstatSyncNoException to fail for non-strings
+# https://github.com/atom/atom-shell/issues/843
+{lstatSyncNoException, statSyncNoException} = fs
+fs.statSyncNoException = (pathToStat) ->
+  return false unless pathToStat and typeof pathToStat is 'string'
+  statSyncNoException(pathToStat)
+fs.lstatSyncNoException = (pathToStat) ->
+  return false unless pathToStat and typeof pathToStat is 'string'
+  lstatSyncNoException(pathToStat)
+
 start = ->
   if process.platform is 'win32'
     SquirrelUpdate = require './squirrel-update'

src/config-schema.coffee

@@ -119,9 +119,6 @@ module.exports =
       autoIndentOnPaste:
         type: 'boolean'
         default: true
-      normalizeIndentOnPaste:
-        type: 'boolean'
-        default: true
       nonWordCharacters:
         type: 'string'
         default: "/\\()\"':,.;<>~!@#$%^&*|+=[]{}`?-"

src/config.coffee

@@ -526,6 +526,9 @@ class Config
 
   # Extended: Restore the global setting at `keyPath` to its default value.
   #
+  # * `scopeSelector` (optional) {String}. eg. '.source.ruby'
+  #   See [the scopes docs](https://atom.io/docs/latest/advanced/scopes-and-scope-descriptors)
+  #   for more information.
   # * `keyPath` The {String} name of the key.
   #
   # Returns the new value.
@@ -721,21 +724,26 @@ class Config
       @configFileHasErrors = false
     catch error
       @configFileHasErrors = true
-      console.error "Failed to load user config '#{@configFilePath}'", error.message
-      console.error error.stack
+      @notifyFailure('Failed to load config.cson', error)
 
   observeUserConfig: ->
     try
       @watchSubscription ?= pathWatcher.watch @configFilePath, (eventType) =>
         @loadUserConfig() if eventType is 'change' and @watchSubscription?
     catch error
-      console.error "Failed to watch user config '#{@configFilePath}'", error.message
-      console.error error.stack
+      @notifyFailure('Failed to watch user config', error)
 
   unobserveUserConfig: ->
     @watchSubscription?.close()
     @watchSubscription = null
 
+  notifyFailure: (errorMessage, error) ->
+    message = "#{errorMessage}"
+    detail = error.stack
+    atom.notifications.addError(message, {detail, closable: true})
+    console.error message
+    console.error detail
+
   save: ->
     allSettings = global: @settings
     allSettings = _.extend allSettings, @scopedSettingsStore.propertiesForSource('user-config')

src/git-repository.coffee

@@ -1,9 +1,8 @@
 {basename, join} = require 'path'
 
 _ = require 'underscore-plus'
-{Subscriber} = require 'emissary'
 EmitterMixin = require('emissary').Emitter
-{Emitter} = require 'event-kit'
+{Emitter, Disposable, CompositeDisposable} = require 'event-kit'
 fs = require 'fs-plus'
 GitUtils = require 'git-utils'
 {deprecate} = require 'grim'
@@ -45,7 +44,6 @@ Task = require './task'
 module.exports =
 class GitRepository
   EmitterMixin.includeInto(this)
-  Subscriber.includeInto(this)
 
   @exists: (path) ->
     if git = @open(path)
@@ -75,6 +73,8 @@ class GitRepository
 
   constructor: (path, options={}) ->
     @emitter = new Emitter
+    @subscriptions = new CompositeDisposable
+
     @repo = GitUtils.open(path)
     unless @repo?
       throw new Error("No Git repository found searching path: #{path}")
@@ -88,13 +88,15 @@ class GitRepository
 
     refreshOnWindowFocus ?= true
     if refreshOnWindowFocus
-      {$} = require './space-pen-extensions'
-      @subscribe $(window), 'focus', =>
+      onWindowFocus = =>
         @refreshIndex()
         @refreshStatus()
 
+      window.addEventListener 'focus', onWindowFocus
+      @subscriptions.add new Disposable(-> window.removeEventListener 'focus', onWindowFocus)
+
     if @project?
-      @subscribe @project.eachBuffer (buffer) => @subscribeToBuffer(buffer)
+      @subscriptions.add @project.eachBuffer (buffer) => @subscribeToBuffer(buffer)
 
   # Public: Destroy this {GitRepository} object.
   #
@@ -109,7 +111,7 @@ class GitRepository
       @repo.release()
       @repo = null
 
-    @unsubscribe()
+    @subscriptions.dispose()
 
   ###
   Section: Event Subscription
@@ -403,10 +405,13 @@ class GitRepository
       if path = buffer.getPath()
         @getPathStatus(path)
 
-    @subscribe buffer.onDidSave(getBufferPathStatus)
-    @subscribe buffer.onDidReload(getBufferPathStatus)
-    @subscribe buffer.onDidChangePath(getBufferPathStatus)
-    @subscribe buffer.onDidDestroy => @unsubscribe(buffer)
+    bufferSubscriptions = new CompositeDisposable
+    bufferSubscriptions.add buffer.onDidSave(getBufferPathStatus)
+    bufferSubscriptions.add buffer.onDidReload(getBufferPathStatus)
+    bufferSubscriptions.add buffer.onDidChangePath(getBufferPathStatus)
+    bufferSubscriptions.add buffer.onDidDestroy =>
+      bufferSubscriptions.dispose()
+      @subscriptions.remove(bufferSubscriptions)
 
   # Subscribes to editor view event.
   checkoutHeadForEditor: (editor) ->

src/grammar-registry.coffee

@@ -2,7 +2,8 @@ _ = require 'underscore-plus'
 {deprecate} = require 'grim'
 {specificity} = require 'clear-cut'
 {Subscriber} = require 'emissary'
-{GrammarRegistry, ScopeSelector} = require 'first-mate'
+FirstMate = require 'first-mate'
+{ScopeSelector} = FirstMate
 ScopedPropertyStore = require 'scoped-property-store'
 PropertyAccessors = require 'property-accessors'
 
@@ -11,20 +12,22 @@ Token = require './token'
 
 # Extended: Syntax class holding the grammars used for tokenizing.
 #
-# An instance of this class is always available as the `atom.syntax` global.
+# An instance of this class is always available as the `atom.grammars` global.
 #
 # The Syntax class also contains properties for things such as the
 # language-specific comment regexes. See {::getProperty} for more details.
 module.exports =
-class Syntax extends GrammarRegistry
+class GrammarRegistry extends FirstMate.GrammarRegistry
   PropertyAccessors.includeInto(this)
   Subscriber.includeInto(this)
-  atom.deserializers.add(this)
 
   @deserialize: ({grammarOverridesByPath}) ->
-    syntax = new Syntax()
-    syntax.grammarOverridesByPath = grammarOverridesByPath
-    syntax
+    grammarRegistry = new GrammarRegistry()
+    grammarRegistry.grammarOverridesByPath = grammarOverridesByPath
+    grammarRegistry
+
+  atom.deserializers.add(this)
+  atom.deserializers.add(name: 'Syntax', deserialize: @deserialize) # Support old serialization
 
   constructor: ->
     super(maxTokensPerLine: 100)
@@ -34,6 +37,17 @@ class Syntax extends GrammarRegistry
 
   createToken: (value, scopes) -> new Token({value, scopes})
 
+  # Extended: Select a grammar for the given file path and file contents.
+  #
+  # This picks the best match by checking the file path and contents against
+  # each grammar.
+  #
+  # * `filePath` A {String} file path.
+  # * `fileContents` A {String} of text for the file path.
+  #
+  # Returns a {Grammar}, never null.
+  selectGrammar: (filePath, fileContents) -> super
+
   # Deprecated: Used by settings-view to display snippets for packages
   @::accessor 'propertyStore', ->
     deprecate("Do not use this. Use a public method on Config")

src/keymap-extensions.coffee

@@ -23,6 +23,10 @@ KeymapManager::loadUserKeymap = ->
   if fs.isFileSync(userKeymapPath)
     @loadKeymap(userKeymapPath, watch: true, suppressErrors: true)
 
+KeymapManager::subscribeToFileReadFailure = ->
+  this.onDidFailToReadFile (error) ->
+    atom.notifications.addError('Failed to load keymap.cson', {detail: error.stack, closable: true})
+
 # This enables command handlers registered via jQuery to call
 # `.abortKeyBinding()` on the `jQuery.Event` object passed to the handler.
 jQuery.Event::abortKeyBinding = ->

src/notification-manager.coffee

@@ -0,0 +1,44 @@
+{Emitter, Disposable} = require 'event-kit'
+Notification = require '../src/notification'
+
+# Experimental: Allows messaging the user. This will likely change, dont use
+# quite yet!
+module.exports =
+class NotificationManager
+  constructor: ->
+    @notifications = []
+    @emitter = new Emitter
+
+  ###
+  Section: Events
+  ###
+
+  onDidAddNotification: (callback) ->
+    @emitter.on 'did-add-notification', callback
+
+  ###
+  Section: Adding Notifications
+  ###
+
+  addSuccess: (message, options) ->
+    @addNotification(new Notification('success', message, options))
+
+  addInfo: (message, options) ->
+    @addNotification(new Notification('info', message, options))
+
+  addWarning: (message, options) ->
+    @addNotification(new Notification('warning', message, options))
+
+  addError: (message, options) ->
+    @addNotification(new Notification('error', message, options))
+
+  addFatalError: (message, options) ->
+    @addNotification(new Notification('fatal', message, options))
+
+  add: (type, message, options) ->
+    @addNotification(new Notification(type, message, options))
+
+  addNotification: (notification) ->
+    @notifications.push(notification)
+    @emitter.emit('did-add-notification', notification)
+    notification

src/notification.coffee

@@ -0,0 +1,33 @@
+
+# Experimental: This will likely change, do not use.
+module.exports =
+class Notification
+  constructor: (@type, @message, @options={}) ->
+    @timestamp = new Date()
+
+  getOptions: -> @options
+
+  getType: -> @type
+
+  getMessage: -> @message
+
+  getTimestamp: -> @timestamp
+
+  getDetail: -> @options.detail
+
+  isEqual: (other) ->
+    @getMessage() == other.getMessage() \
+      and @getType() == other.getType() \
+      and @getDetail() == other.getDetail()
+
+  isClosable: ->
+    !!@options.closable
+
+  getIcon: ->
+    return @options.icon if @options.icon?
+    switch @type
+      when 'fatal' then 'bug'
+      when 'error' then 'flame'
+      when 'warning' then 'alert'
+      when 'info' then 'info'
+      when 'success' then 'check'

src/package.coffee

@@ -254,7 +254,7 @@ class Package
     grammarPaths = fs.listSync(grammarsDirPath, ['json', 'cson'])
     for grammarPath in grammarPaths
       try
-        grammar = atom.syntax.readGrammarSync(grammarPath)
+        grammar = atom.grammars.readGrammarSync(grammarPath)
         grammar.packageName = @name
         @grammars.push(grammar)
         grammar.activate()
@@ -268,7 +268,7 @@ class Package
     return Q() if @grammarsLoaded
 
     loadGrammar = (grammarPath, callback) =>
-      atom.syntax.readGrammar grammarPath, (error, grammar) =>
+      atom.grammars.readGrammar grammarPath, (error, grammar) =>
         if error?
           console.warn("Failed to load grammar: #{grammarPath}", error.stack ? error)
         else

src/pane-element.coffee

@@ -95,7 +95,7 @@ class PaneElement extends HTMLElement
 
   itemRemoved: ({item, index, destroyed}) ->
     if viewToRemove = @model.getView(item)
-      callRemoveHooks(viewToRemove)
+      callRemoveHooks(viewToRemove) if destroyed
       viewToRemove.remove()
 
   paneDestroyed: ->

src/panel-container-element.coffee

@@ -15,10 +15,15 @@ class PanelContainerElement extends HTMLElement
   panelAdded: ({panel, index}) ->
     panelElement = panel.getView()
     panelElement.classList.add(@model.getLocation())
+    if @model.isModal()
+      panelElement.classList.add("overlay", "from-top")
+    else
+      panelElement.classList.add("tool-panel", "panel-#{@model.getLocation()}")
+
     if index >= @childNodes.length
       @appendChild(panelElement)
     else
-      referenceItem = @childNodes[index + 1]
+      referenceItem = @childNodes[index]
       @insertBefore(panelElement, referenceItem)
 
     if @model.isModal()

src/selection.coffee

@@ -359,8 +359,11 @@ class Selection extends Model
     @clear()
     @cursor.needsAutoscroll = @cursor.isLastCursor()
 
+    precedingText = @editor.getTextInRange([[oldBufferRange.start.row, 0], oldBufferRange.start])
+    startLevel = @editor.indentLevelForLine(precedingText)
+
     if options.indentBasis? and not options.autoIndent
-      text = @normalizeIndents(text, options.indentBasis)
+      text = @adjustIndent(text, startLevel - options.indentBasis)
 
     newBufferRange = @editor.buffer.setTextInRange(oldBufferRange, text, pick(options, 'undo', 'normalizeLineEndings'))
 
@@ -562,8 +565,10 @@ class Selection extends Model
   #   cursor's horizontal position. (default: false)
   copy: (maintainClipboard=false, fullLine=false) ->
     return if @isEmpty()
-    selectionText = @editor.buffer.getTextInRange(@getBufferRange())
-    selectionIndentation = @editor.indentationForBufferRow(@getBufferRange().start.row)
+    {start, end} = @getBufferRange()
+    selectionText = @editor.getTextInRange([start, end])
+    precedingText = @editor.getTextInRange([[start.row, 0], start])
+    startLevel = @editor.indentLevelForLine(precedingText)
 
     if maintainClipboard
       {text: clipboardText, metadata} = atom.clipboard.readWithMetadata()
@@ -572,16 +577,17 @@ class Selection extends Model
         metadata.selections = [{
           text: clipboardText,
           indentBasis: metadata.indentBasis,
+          fullLine: metadata.fullLine,
         }]
       metadata.selections.push({
         text: selectionText,
-        indentBasis: selectionIndentation,
+        indentBasis: startLevel,
         fullLine: fullLine
       })
       atom.clipboard.write([clipboardText, selectionText].join("\n"), metadata)
     else
       atom.clipboard.write(selectionText, {
-        indentBasis: selectionIndentation,
+        indentBasis: startLevel,
         fullLine: fullLine
       })
 
@@ -591,34 +597,22 @@ class Selection extends Model
     @editor.createFold(range.start.row, range.end.row)
     @cursor.setBufferPosition([range.end.row + 1, 0])
 
-  # Public: Indents the given text to the suggested level based on the grammar.
+  # Public: Increases the indentation level of
   #
-  # * `text` The {String} to indent within the selection.
-  # * `indentBasis` The beginning indent level.
-  normalizeIndents: (text, indentBasis) ->
-    textPrecedingCursor = @cursor.getCurrentBufferLine()[0...@cursor.getBufferColumn()]
-    isCursorInsideExistingLine = /\S/.test(textPrecedingCursor)
 
+  # * `indentIncrease` The beginning indent level.
+  adjustIndent: (text, indentIncrease) ->
     lines = text.split('\n')
-    firstLineIndentLevel = @editor.indentLevelForLine(lines[0])
-    if isCursorInsideExistingLine
-      minimumIndentLevel = @editor.indentationForBufferRow(@cursor.getBufferRow())
-    else
-      minimumIndentLevel = @cursor.getIndentLevel()
-
-    normalizedLines = []
-    for line, i in lines
-      if i == 0
-        indentLevel = 0
-      else if line == '' # remove all indentation from empty lines
-        indentLevel = 0
+    for line, i in lines when i > 0
+      if indentIncrease == 0
+        continue
+      else if indentIncrease > 0
+        lines[i] = @editor.buildIndentString(indentIncrease) + line
       else
-        lineIndentLevel = @editor.indentLevelForLine(lines[i])
-        indentLevel = minimumIndentLevel + (lineIndentLevel - indentBasis)
-
-      normalizedLines.push(@setIndentationForLine(line, indentLevel))
-
-    normalizedLines.join('\n')
+        currentIndentLevel = @editor.indentLevelForLine(lines[i])
+        indentLevel = Math.max(0, currentIndentLevel + indentIncrease)
+        lines[i] = line.replace(/^[\t ]+/, @editor.buildIndentString(indentLevel))
+    lines.join('\n')
 
   # Indent the current line(s).
   #
@@ -651,11 +645,6 @@ class Selection extends Model
     for row in [start..end]
       @editor.buffer.insert([row, 0], @editor.getTabText()) unless @editor.buffer.lineLengthForRow(row) == 0
 
-  setIndentationForLine: (line, indentLevel) ->
-    desiredIndentLevel = Math.max(0, indentLevel)
-    desiredIndentString = @editor.buildIndentString(desiredIndentLevel)
-    line.replace(/^[\t ]*/, desiredIndentString)
-
   ###
   Section: Managing multiple selections
   ###

src/space-pen-extensions.coffee

@@ -12,7 +12,7 @@ jQuery.cleanData = (elements) ->
 
 SpacePenCallRemoveHooks = SpacePen.callRemoveHooks
 SpacePen.callRemoveHooks = (element) ->
-  view.unsubscribe() for view in SpacePen.viewsForElement(element)
+  view.unsubscribe?() for view in SpacePen.viewsForElement(element)
   SpacePenCallRemoveHooks(element)
 
 NativeEventNames = new Set

src/text-editor-component.coffee

@@ -199,7 +199,6 @@ TextEditorComponent = React.createClass
   componentWillUnmount: ->
     {editor, hostElement} = @props
 
-    hostElement.__spacePenView.trigger 'editor:will-be-removed', [hostElement.__spacePenView]
     @unsubscribe()
     @scopedConfigSubscriptions.dispose()
     window.removeEventListener 'resize', @requestHeightAndWidthMeasurement

src/text-editor-element.coffee

@@ -103,7 +103,9 @@ class TextEditorElement extends HTMLElement
     )
     @component = React.renderComponent(@componentDescriptor, @rootElement)
 
-    unless @useShadowDOM
+    if @useShadowDOM
+      @shadowRoot.addEventListener('blur', @shadowRootBlurred.bind(this), true)
+    else
       inputNode = @component.refs.input.getDOMNode()
       inputNode.addEventListener 'focus', @focused.bind(this)
       inputNode.addEventListener 'blur', => @dispatchEvent(new FocusEvent('blur', bubbles: false))
@@ -128,6 +130,16 @@ class TextEditorElement extends HTMLElement
 
     @component?.blurred()
 
+  # Work around what seems to be a bug in Chromium. Focus can be stolen from the
+  # hidden input when clicking on the gutter and transferred to the
+  # already-focused host element. The host element never gets a 'focus' event
+  # however, which leaves us in a limbo state where the text editor element is
+  # focused but the hidden input isn't focused. This always refocuses the hidden
+  # input if a blur event occurs in the shadow DOM that is transferring focus
+  # back to the host element.
+  shadowRootBlurred: (event) ->
+    @component.focused() if event.relatedTarget is this
+
   addGrammarScopeAttribute: ->
     grammarScope = @model.getGrammar()?.scopeName?.replace(/\./g, ' ')
     @dataset.grammar = grammarScope

src/text-editor-view.coffee

@@ -138,6 +138,7 @@ class TextEditorView extends View
 
   beforeRemove: ->
     @trigger 'editor:detached', [this]
+    @trigger 'editor:will-be-removed', [this]
     @attached = false
 
   remove: (selector, keepData) ->

src/text-editor.coffee

@@ -1098,34 +1098,49 @@ class TextEditor extends Model
   # abort the transaction, call {::abortTransaction} to terminate the function's
   # execution and revert any changes performed up to the abortion.
   #
-  # * `groupingInterval` (optional) This is the sames as the `groupingInterval`
-  #    parameter in {::beginTransaction}
-  # * `fn` A {Function} to call inside the transaction.
-  transact: (groupingInterval, fn) -> @buffer.transact(groupingInterval, fn)
-
-  # Extended: Start an open-ended transaction.
-  #
-  # Call {::commitTransaction} or {::abortTransaction} to terminate the
-  # transaction. If you nest calls to transactions, only the outermost
-  # transaction is considered. You must match every begin with a matching
-  # commit, but a single call to abort will cancel all nested transactions.
-  #
   # * `groupingInterval` (optional) The {Number} of milliseconds for which this
   #   transaction should be considered 'groupable' after it begins. If a transaction
   #   with a positive `groupingInterval` is committed while the previous transaction is
   #   still 'groupable', the two transactions are merged with respect to undo and redo.
+  # * `fn` A {Function} to call inside the transaction.
+  transact: (groupingInterval, fn) -> @buffer.transact(groupingInterval, fn)
+
+  # Deprecated: Start an open-ended transaction.
   beginTransaction: (groupingInterval) -> @buffer.beginTransaction(groupingInterval)
 
-  # Extended: Commit an open-ended transaction started with {::beginTransaction}
-  # and push it to the undo stack.
-  #
-  # If transactions are nested, only the outermost commit takes effect.
+  # Deprecated: Commit an open-ended transaction started with {::beginTransaction}.
   commitTransaction: -> @buffer.commitTransaction()
 
   # Extended: Abort an open transaction, undoing any operations performed so far
   # within the transaction.
   abortTransaction: -> @buffer.abortTransaction()
 
+  # Extended: Create a pointer to the current state of the buffer for use
+  # with {::revertToCheckpoint} and {::groupChangesSinceCheckpoint}.
+  #
+  # Returns a checkpoint value.
+  createCheckpoint: -> @buffer.createCheckpoint()
+
+  # Extended: Revert the buffer to the state it was in when the given
+  # checkpoint was created.
+  #
+  # The redo stack will be empty following this operation, so changes since the
+  # checkpoint will be lost. If the given checkpoint is no longer present in the
+  # undo history, no changes will be made to the buffer and this method will
+  # return `false`.
+  #
+  # Returns a {Boolean} indicating whether the operation succeeded.
+  revertToCheckpoint: (checkpoint) -> @buffer.revertToCheckpoint(checkpoint)
+
+  # Extended: Group all changes since the given checkpoint into a single
+  # transaction for purposes of undo/redo.
+  #
+  # If the given checkpoint is no longer present in the undo history, no
+  # grouping will be performed and this method will return `false`.
+  #
+  # Returns a {Boolean} indicating whether the operation succeeded.
+  groupChangesSinceCheckpoint: (checkpoint) -> @buffer.groupChangesSinceCheckpoint(checkpoint)
+
   ###
   Section: TextEditor Coordinates
   ###

src/theme-manager.coffee

@@ -334,13 +334,15 @@ class ThemeManager
   isInitialLoadComplete: -> @initialLoadComplete
 
   addActiveThemeClasses: ->
+    workspaceElement = atom.views.getView(atom.workspace)
     for pack in @getActiveThemes()
-      atom.workspaceView?[0]?.classList.add("theme-#{pack.name}")
+      workspaceElement.classList.add("theme-#{pack.name}")
     return
 
   removeActiveThemeClasses: ->
+    workspaceElement = atom.views.getView(atom.workspace)
     for pack in @getActiveThemes()
-      atom.workspaceView?[0]?.classList.remove("theme-#{pack.name}")
+      workspaceElement.classList.remove("theme-#{pack.name}")
     return
 
   refreshLessCache: ->

src/tokenized-buffer.coffee

@@ -26,8 +26,8 @@ class TokenizedBuffer extends Model
   constructor: ({@buffer, @tabLength, @invisibles}) ->
     @emitter = new Emitter
 
-    @subscribe atom.syntax.onDidAddGrammar(@grammarAddedOrUpdated)
-    @subscribe atom.syntax.onDidUpdateGrammar(@grammarAddedOrUpdated)
+    @subscribe atom.grammars.onDidAddGrammar(@grammarAddedOrUpdated)
+    @subscribe atom.grammars.onDidUpdateGrammar(@grammarAddedOrUpdated)
 
     @subscribe @buffer.preemptDidChange (e) => @handleBufferChange(e)
     @subscribe @buffer.onDidChangePath (@bufferPath) => @reloadGrammar()
@@ -98,7 +98,7 @@ class TokenizedBuffer extends Model
     @emitter.emit 'did-change-grammar', grammar
 
   reloadGrammar: ->
-    if grammar = atom.syntax.selectGrammar(@buffer.getPath(), @buffer.getText())
+    if grammar = atom.grammars.selectGrammar(@buffer.getPath(), @buffer.getText())
       @setGrammar(grammar)
     else
       throw new Error("No grammar found for path: #{path}")

src/tooltip-manager.coffee

@@ -0,0 +1,60 @@
+_ = require 'underscore-plus'
+{Disposable} = require 'event-kit'
+{$} = require './space-pen-extensions'
+
+# Essential: Associates tooltips with HTML elements or selectors.
+module.exports =
+class TooltipManager
+  defaults:
+    delay:
+      show: 1000
+      hide: 100
+    container: 'body'
+    html: true
+    placement: 'auto top'
+    viewportPadding: 2
+
+  # Essential: Add a tooltip to the given element.
+  #
+  # * `target` An `HTMLElement`
+  # * `options` See http://getbootstrap.com/javascript/#tooltips for a full list
+  #   of options. You can also supply the following additional options:
+  #   * `title` {String} Text in the tip.
+  #   * `keyBindingCommand` A {String} containing a command name. If you specify
+  #     this option and a key binding exists that matches the command, it will
+  #     be appended to the title or rendered alone if no title is specified.
+  #   * `keyBindingTarget` An `HTMLElement` on which to look up the key binding.
+  #     If this option is not supplied, the first of all matching key bindings
+  #     for the given command will be rendered.
+  #
+  # Returns a {Disposable} on which `.dispose()` can be called to remove the
+  # tooltip.
+  add: (target, options) ->
+    requireBootstrapTooltip()
+
+    {keyBindingCommand, keyBindingTarget} = options
+
+    if keyBindingCommand?
+      bindings = atom.keymaps.findKeyBindings(command: keyBindingCommand, target: keyBindingTarget)
+      if options.title?
+        options.title += " " + getKeystroke(bindings)
+      else
+        options.title = getKeystroke(bindings)
+
+    $target = $(target)
+    $target.tooltip(_.defaults(options, @defaults))
+
+    new Disposable -> $target.tooltip('destroy')
+
+humanizeKeystrokes = (keystroke) ->
+  keystrokes = keystroke.split(' ')
+  keystrokes = (_.humanizeKeystroke(stroke) for stroke in keystrokes)
+  keystrokes.join(' ')
+
+getKeystroke = (bindings) ->
+  if bindings?.length
+    "<span class=\"keystroke\">#{humanizeKeystrokes(bindings[0].keystrokes)}</span>"
+  else
+
+requireBootstrapTooltip = _.once ->
+  atom.requireWithGlobals('bootstrap/js/tooltip', {jQuery: $})

src/view-registry.coffee

@@ -89,22 +89,22 @@ class ViewRegistry
   #
   # ## Examples
   #
-  # ### Getting An Editor View
+  # ### Getting An Editor Element
   # ```coffee
   # textEditor = atom.workspace.getActiveTextEditor()
-  # textEditorView = atom.views.getView(textEditor)
+  # textEditorElement = atom.views.getView(textEditor)
   # ```
   #
-  # ### Getting A Pane View
+  # ### Getting A Pane Element
   # ```coffee
   # pane = atom.workspace.getActivePane()
-  # paneView = atom.views.getView(pane)
+  # paneElement = atom.views.getView(pane)
   # ```
   #
-  # ### Getting The Workspace View
+  # ### Getting The Workspace Element
   #
   # ```coffee
-  # workspaceView = atom.views.getView(atom.workspace)
+  # workspaceElement = atom.views.getView(atom.workspace)
   # ```
   #
   # * `object` The object for which you want to retrieve a view. This can be a

src/window-event-handler.coffee

@@ -15,11 +15,13 @@ class WindowEventHandler
     @reloadRequested = false
 
     @subscribe ipc, 'command', (command, args...) ->
+
       activeElement = document.activeElement
-      # Use root view if body has focus
-      if activeElement is document.body and atom.workspaceView?
-        activeElement = atom.workspaceView
-      $(activeElement).trigger(command, args...)
+      # Use the workspace element view if body has focus
+      if activeElement is document.body and workspaceElement = atom.views.getView(atom.workspace)
+        activeElement = workspaceElement
+
+      atom.commands.dispatch(activeElement, command, args[0])
 
     @subscribe ipc, 'context-command', (command, args...) ->
       $(atom.contextMenu.activeElement).trigger(command, args...)

src/workspace.coffee

@@ -105,13 +105,13 @@ class Workspace extends Model
 
       packageNames.push(packageName)
       for scopeName in includedGrammarScopes ? []
-        addGrammar(atom.syntax.grammarForScopeName(scopeName))
+        addGrammar(atom.grammars.grammarForScopeName(scopeName))
 
     editors = @getTextEditors()
     addGrammar(editor.getGrammar()) for editor in editors
 
     if editors.length > 0
-      for grammar in atom.syntax.getGrammars() when grammar.injectionSelector
+      for grammar in atom.grammars.getGrammars() when grammar.injectionSelector
         addGrammar(grammar)
 
     _.uniq(packageNames)
@@ -682,8 +682,6 @@ class Workspace extends Model
   #
   # Returns a {Panel}
   addModalPanel: (options={}) ->
-    # TODO: remove these default classes. They are to supoprt existing themes.
-    options.className ?= 'overlay from-top'
     @addPanel('modal', options)
 
   addPanel: (location, options) ->

static/index.js

@@ -2,8 +2,26 @@ window.onload = function() {
   try {
     var startTime = Date.now();
 
+    var fs = require('fs');
     var path = require('path');
 
+    // Patch fs.statSyncNoException/fs.lstatSyncNoException to fail for non-strings
+    // https://github.com/atom/atom-shell/issues/843
+    var statSyncNoException = fs.statSyncNoException;
+    var lstatSyncNoException = fs.lstatSyncNoException;
+    fs.statSyncNoException = function(pathToStat) {
+      if (pathToStat && typeof pathToStat === 'string')
+        return statSyncNoException(pathToStat);
+      else
+        return false;
+    };
+    fs.lstatSyncNoException = function(pathToStat) {
+      if (pathToStat && typeof pathToStat === 'string')
+        return lstatSyncNoException(pathToStat);
+      else
+        return false;
+    };
+
     // Skip "?loadSettings=".
     var loadSettings = JSON.parse(decodeURIComponent(location.search.substr(14)));
 

static/jasmine.less

@@ -136,7 +136,14 @@ body {
   }
 
   .result-message.deprecation-message {
-    color: #f0ad4e;
+    font-weight: normal;
+    color: darken(#f0ad4e, 20%);
+    line-height: 1.4;
+
+    code {
+      color: darken(#f0ad4e, 20%);
+      background: lighten(#f0ad4e, 35%);
+    }
   }
 
   .stack-trace {

static/utilities.less

@@ -64,13 +64,3 @@ div > .inline-block-tight:last-child {
     margin-left: 0;
   }
 }
-
-.error {
-  -webkit-animation: flash-error 0.3s ease-in;
-}
-
-@-webkit-keyframes flash-error {
-  0% { background: @background-color-error; }
-
-  100% { background: auto; }
-}